Rafael Sanjuan

Summary

Affiliation: University of Valencia
Country: Spain

Publications

  1. doi request reprint Experimental evolution of RNA versus DNA viruses
    Pilar 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
  2. pmc Mechanisms of viral mutation
    Rafael Sanjuan
    Department of Genetics and Institute for Integrative Systems Biology I2SysBio, Universitat de Valencia, C Catedrático José Beltrán 2, 46980, Paterna, Valencia, Spain
    Cell Mol Life Sci 73:4433-4448. 2016
  3. doi request reprint Evolution of oncolytic viruses
    Rafael Sanjuan
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Valencia, Spain Electronic address
    Curr Opin Virol 13:1-5. 2015
  4. pmc Variation in RNA virus mutation rates across host cells
    Marine Combe
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Valencia, Spain
    PLoS Pathog 10:e1003855. 2014
  5. pmc Immune activation promotes evolutionary conservation of T-cell epitopes in HIV-1
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    PLoS Biol 11:e1001523. 2013
  6. pmc From molecular genetics to phylodynamics: evolutionary relevance of mutation rates across viruses
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Paterna, Spain
    PLoS Pathog 8:e1002685. 2012
  7. pmc Viral mutation rates
    Rafael 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
  8. doi request reprint Interplay between RNA structure and protein evolution in HIV-1
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departamento de Genética, Universitat de Valencia, Spain
    Mol Biol Evol 28:1333-8. 2011
  9. pmc A network model for the correlation between epistasis and genomic complexity
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    PLoS ONE 3:e2663. 2008
  10. pmc Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies
    Rafael 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

Collaborators

Detail Information

Publications47

  1. doi request reprint Experimental evolution of RNA versus DNA viruses
    Pilar 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...
  2. pmc Mechanisms of viral mutation
    Rafael Sanjuan
    Department of Genetics and Institute for Integrative Systems Biology I2SysBio, Universitat de Valencia, C Catedrático José Beltrán 2, 46980, Paterna, Valencia, Spain
    Cell Mol Life Sci 73:4433-4448. 2016
    ..Our current knowledge of viral mutation rates indicates that viral genetic diversity is determined by multiple virus- and host-dependent processes, and that viral mutation rates can evolve in response to specific selective pressures...
  3. doi request reprint Evolution of oncolytic viruses
    Rafael Sanjuan
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Valencia, Spain Electronic address
    Curr Opin Virol 13:1-5. 2015
    ..Directed evolution provides an alternative approach that may help to obtain new OVs without prejudice toward the underlying molecular mechanisms involved. ..
  4. pmc Variation in RNA virus mutation rates across host cells
    Marine Combe
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Valencia, Spain
    PLoS Pathog 10:e1003855. 2014
    ..This may contribute to explaining the relatively slow evolution of VSV and other arthropod-borne viruses in nature. ..
  5. pmc Immune activation promotes evolutionary conservation of T-cell epitopes in HIV-1
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, 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...
  6. pmc From molecular genetics to phylodynamics: evolutionary relevance of mutation rates across viruses
    Rafael 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...
  7. pmc Viral mutation rates
    Rafael 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...
  8. doi request reprint Interplay between RNA structure and protein evolution in HIV-1
    Rafael 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...
  9. pmc A network model for the correlation between epistasis and genomic complexity
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    PLoS ONE 3:e2663. 2008
    ....
  10. pmc Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies
    Rafael 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...
  11. pmc The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus
    Rafael 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...
  12. ncbi request reprint Weighted least-squares likelihood ratio test for branch testing in phylogenies reconstructed from distance measures
    Rafael 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...
  13. ncbi request reprint In silico predicted robustness of viroid RNA secondary structures. II. Interaction between mutation pairs
    Rafael 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...
  14. pmc Epistasis and the adaptability of an RNA virus
    Rafael 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...
  15. ncbi request reprint In silico predicted robustness of viroids RNA secondary structures. I. The effect of single mutations
    Rafael 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...
  16. ncbi request reprint Natural selection and the organ-specific differentiation of HIV-1 V3 hypervariable region
    Rafael 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...
  17. pmc The fitness effects of random mutations in single-stranded DNA and RNA bacteriophages
    Pilar 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...
  18. pmc The effect of genetic robustness on evolvability in digital organisms
    Santiago 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)...
  19. pmc The cost of replication fidelity in an RNA virus
    Victoria 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...
  20. doi request reprint Highly heterogeneous mutation rates in the hepatitis C virus genome
    Ron Geller
    Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology I2SysBio, Universitat de Valencia, 46980 Paterna, Valencia, Spain
    Nat Microbiol 1:16045. 2016
    ..These data provide a site-wise baseline for interrogating natural selection, genetic load and evolvability in HCV, as well as for evaluating drug resistance and immune evasion risks. ..
  21. pmc Selection for robustness in mutagenized RNA viruses
    Rafael 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...
  22. pmc The contribution of epistasis to the architecture of fitness in an RNA virus
    Rafael 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...
  23. pmc Relationship between within-host fitness and virulence in the vesicular stomatitis virus: correlation with partial decoupling
    Victoria Furió
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Spain
    J Virol 86:12228-36. 2012
    ....
  24. pmc Effect of ribavirin on the mutation rate and spectrum of hepatitis C virus in vivo
    José 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...
  25. ncbi request reprint The effect of co- and superinfection on the adaptive dynamics of vesicular stomatitis virus
    Francy 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
    ....
  26. ncbi request reprint Mode of selection and experimental evolution of antiviral drugs resistance in vesicular stomatitis virus
    José 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...
  27. pmc Delayed lysis confers resistance to the nucleoside analogue 5-fluorouracil and alleviates mutation accumulation in the single-stranded DNA bacteriophage ϕX174
    Marianoel Pereira-Gómez
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    J Virol 88:5042-9. 2014
    ..This form of mutation rate regulation may also be utilized by other viruses whose replication mode is similar to that of bacteriophage ϕX174...
  28. pmc Distribution of fitness effects caused by single-nucleotide substitutions in bacteriophage f1
    Joan 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...
  29. pmc Nucleoside analogue mutagenesis of a single-stranded DNA virus: evolution and resistance
    Pilar 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...
  30. pmc The cost of replication fidelity in human immunodeficiency virus type 1
    Victoria 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...
  31. doi request reprint Enhanced adaptation of vesicular stomatitis virus in cells infected with vaccinia virus
    Francy 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...
  32. doi request reprint Human norovirus hyper-mutation revealed by ultra-deep sequencing
    José M Cuevas
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
    Infect Genet Evol 41:233-9. 2016
    ..The type of changes produced and their sequence context are compatible with ADAR-mediated editing of the viral RNA. ..
  33. pmc The external domains of the HIV-1 envelope are a mutational cold spot
    Ron Geller
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de Valencia, C Catedrático José Beltrán 2, Paterna, 46980 Valencia, Spain
    Nat Commun 6:8571. 2015
    ....
  34. pmc Single-Cell Analysis of RNA Virus Infection Identifies Multiple Genetically Diverse Viral Genomes within Single Infectious Units
    Marine Combe
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de Valencia, C Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain
    Cell Host Microbe 18:424-32. 2015
    ..These results unravel genetic and structural features of a virus at the single-cell level, with implications for viral diversity and evolution. ..
  35. pmc Correlation between mutation rate and genome size in riboviruses: mutation rate of bacteriophage Qβ
    Katie Bradwell
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de Valencia 46980, Spain
    Genetics 195:243-51. 2013
    ..We suggest that the mutation rates of RNA viruses might be optimized for maximal adaptability and that the value of this optimum may in turn depend inversely on genome size. ..
  36. pmc Point mutation rate of bacteriophage PhiX174
    José 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)...
  37. pmc Constrained evolvability of interferon suppression in an RNA virus
    Raquel Garijo
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Valencia, Spain
    Sci Rep 6:24722. 2016
    ..Our results thus suggest that virus-virus interactions and alternative strategies of innate immunity evasion can determine the evolution of IFN suppression in a virus. ..
  38. pmc Experimental evolution of an RNA virus in cells with innate immunity defects
    Pablo Hernández-Alonso
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Paterna 46980, Spain
    Virus Evol 1:vev008. 2015
    ..However, this process is not deterministic at the molecular level, probably because the fixation of mutations which are tolerated under a relaxed selection regime is governed mainly by random genetic drift...
  39. pmc Extremely High Mutation Rate of HIV-1 In Vivo
    José M Cuevas
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Valencia, Spain
    PLoS Biol 13:e1002251. 2015
    ..However, the amount of A3-mediated editing varies broadly, and we find that low-edited sequences are more abundant among rapid progressors, suggesting that suboptimal A3 activity might enhance HIV-1 genetic diversity and pathogenesis. ..
  40. ncbi request reprint The fitness effects of synonymous mutations in DNA and RNA viruses
    José 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...
  41. doi request reprint Mutation rate of bacteriophage ΦX174 modified through changes in GATC sequence context
    José 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...
  42. doi request reprint Unequal distribution of RT-PCR artifacts along the E1-E2 region of Hepatitis C virus
    Pilar 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...
  43. pmc Effect of mismatch repair on the mutation rate of bacteriophage ϕX174
    Marianoel Pereira-Gómez
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Paterna 46980, Spain
    Virus Evol 1:vev010. 2015
    ....
  44. pmc Lamivudine/Adefovir Treatment Increases the Rate of Spontaneous Mutation of Hepatitis B Virus in Patients
    Marianoel Pereira-Gómez
    Institute for Integrative Systems Biology I2SysBio, Universitat de Valencia, Valencia, Spain
    PLoS ONE 11:e0163363. 2016
    ..Based on these data, the rate at which HBV produces new genetic variants in treated patients is similar to or even higher than in RNA viruses. ..
  45. pmc Genome-Wide Estimation of the Spontaneous Mutation Rate of Human Adenovirus 5 by High-Fidelity Deep Sequencing
    Jennifer Risso-Ballester
    Institute for Integrative Systems Biology I2SysBio, Universitat de València and Consejo Superior de Investigaciones Científicas, Valencia, Spain
    PLoS Pathog 12:e1006013. 2016
    ..Third, mutation probability increased at GpC dinucleotides. Our findings suggest that host factors may influence the distribution of spontaneous mutations in human adenoviruses and potentially other nuclear DNA viruses...
  46. pmc Experimental evolution of an oncolytic vesicular stomatitis virus with increased selectivity for p53-deficient cells
    Raquel Garijo
    Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Valencia, Spain Center for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
    PLoS ONE 9:e102365. 2014
    ..Our results show that RNA viruses can be specifically adapted typical cancer features such as p53 inactivation, and illustrate the usefulness of experimental evolution for oncolytic virotherapy. ..
  47. ncbi request reprint [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...