All Stories

  1. Rodents as potential reservoirs for toroviruses

    Article • Virology Journal, September 2025, Springer Science + Business Media

    PhD José Manuel Cuevas

  2. Identification and characterization of novel bat coronaviruses in Spain

    Article • PLoS Pathogens, August 2025, PLOS

    PhD José Manuel Cuevas

  3. Complete Genomes of DNA Viruses in Fecal Samples from Small Terrestrial Mammals in Spain

    Article • Viruses, December 2024, MDPI AG

    PhD José Manuel Cuevas

  4. Complete genomes of DNA viruses in faecal samples from small terrestrial mammals in Spain

    Article • November 2024, Cold Spring Harbor Laboratory Press

    PhD José Manuel Cuevas

  5. Phylogenetic evidence supporting the nonenveloped nature of hepadnavirus ancestors

    Article • Proceedings of the National Academy of Sciences, October 2024, Proceedings of the National Academy of Sciences

    PhD José Manuel Cuevas

  6. Genetic diversity and cross-species transmissibility of bat-associated picornaviruses from Spain

    Article • Virology Journal, August 2024, Springer Science + Business Media

    PhD José Manuel Cuevas

  7. Full-genome sequencing of dozens of new DNA viruses found in Spanish bat feces

    Article • Microbiology Spectrum, August 2024, ASM Journals

    PhD José Manuel Cuevas

  8. A new clade of pararetroviruses distantly related to hepadnaviruses and nackednaviruses

    Article • August 2024, Cold Spring Harbor Laboratory Press

    PhD José Manuel Cuevas

  9. Genetic diversity and cross-species transmissibility of bat-associated picornaviruses from Spain

    Article • June 2024, Cold Spring Harbor Laboratory Press

    PhD José Manuel Cuevas

  10. SARS-CoV-2 remodels the landscape of small non-coding RNAs with infection time and symptom severity

    Article • npj Systems Biology and Applications, April 2024, Springer Science + Business Media

    PhD José Manuel Cuevas

  11. Optimized Recovery of Viral DNA and RNA from Blood Plasma for Viral Metagenomics

    Article • December 2023, Springer Science + Business Media

    PhD José Manuel Cuevas

  12. Human Anelloviruses: Influence of Demographic Factors, Recombination, and Worldwide Diversity

    Article • Microbiology Spectrum, June 2023, ASM Journals

    PhD José Manuel Cuevas

  13. Exploring the Diversity of the Human Blood Virome

    Article • Viruses, November 2021, MDPI AG

    PhD José Manuel Cuevas

  14. Deep viral blood metagenomics reveals extensive anellovirus diversity in healthy humans

    Article • Scientific Reports, March 2021, Springer Science + Business Media

    PhD José Manuel Cuevas

  15. Genome-scale analysis of evolutionary rate and selection in a fast-expanding Spanish cluster of HIV-1 subtype F1

    Article • Infection Genetics and Evolution, December 2018, Elsevier

    PhD José Manuel Cuevas

  16. Role of APOBEC3H in the Viral Control of HIV Elite Controller Patients

    Article • International Journal of Medical Sciences, January 2018, Ivyspring International Publisher

    PhD José Manuel Cuevas

  17. A putative antiviral role of plant cytidine deaminases

    Article • F1000Research, June 2017, Faculty of 1000, Ltd.

    Professor Santiago F Elena, PhD José Manuel Cuevas

  18. Multi-virion infectious units arise from free viral particles in an enveloped virus

    Article • Nature Microbiology, May 2017, Springer Science + Business Media

    PhD José Manuel Cuevas

  19. A putative antiviral role of plant cytidine deaminases

    Article • F1000Research, May 2017, Faculty of 1000, Ltd.

    Professor Santiago F Elena, Dr Ana Grande-Perez, PhD José Manuel Cuevas

  20. Genome-Wide Estimation of the Spontaneous Mutation Rate of Human Adenovirus 5 by High-Fidelity Deep Sequencing

    Article • PLoS Pathogens, November 2016, PLOS

    PhD José Manuel Cuevas

  21. Human norovirus hyper-mutation revealed by ultra-deep sequencing

    Article • Infection Genetics and Evolution, July 2016, Elsevier

    Dr Jesús Rodríguez Díaz, PhD José Manuel Cuevas

  22. The transcriptomics of an experimentally evolved plant-virus interaction

    Article • Scientific Reports, April 2016, Nature

    Professor Santiago F Elena, PhD José Manuel Cuevas

  23. Constrained evolvability of interferon suppression in an RNA virus

    Article • Scientific Reports, April 2016, Springer Science + Business Media

    PhD José Manuel Cuevas

  24. Highly heterogeneous mutation rates in the hepatitis C virus genome

    Article • Nature Microbiology, April 2016, Nature

    Antonio Mas, PhD José Manuel Cuevas

  25. The external domains of the HIV-1 envelope are a mutational cold spot

    Article • Nature Communications, October 2015, Springer Science + Business Media

    PhD José Manuel Cuevas

  26. Single-Cell Analysis of RNA Virus Infection Identifies Multiple Genetically Diverse Viral Genomes within Single Infectious Units

    Article • Cell Host & Microbe, October 2015, Elsevier

    PhD José Manuel Cuevas

  27. Extremely High Mutation Rate of HIV-1 In Vivo

    Article • PLoS Biology, September 2015, PLOS

    PhD José Manuel Cuevas

  28. Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host

    Article • Philosophical Transactions of the Royal Society B Biological Sciences, July 2015, Royal Society Publishing

    Professor Santiago F Elena, PhD José Manuel Cuevas

  29. Temporal Dynamics of Intrahost Molecular Evolution for a Plant RNA Virus

    Article • Molecular Biology and Evolution, February 2015, Oxford University Press (OUP)

    Professor Santiago F Elena, PhD José Manuel Cuevas

  30. BrazilianPotato virus Yisolates identified as members of a new clade facilitate the reconstruction of evolutionary traits within this species

    Article • Plant Pathology, January 2015, Wiley

    Professor Santiago F Elena, PhD José Manuel Cuevas

  31. EXPERIMENTAL EVOLUTION OF AN EMERGING PLANT VIRUS IN HOST GENOTYPES THAT DIFFER IN THEIR SUSCEPTIBILITY TO INFECTION

    Article • Evolution, July 2014, Oxford University Press (OUP)

    Professor Santiago F Elena, Dr Sergi Valverde, PhD José Manuel Cuevas

  32. Intra-specific variability and biological relevance of P3N-PIPO protein length in potyviruses

    Article • BMC Evolutionary Biology, November 2013, Springer Science + Business Media

    Professor Santiago F Elena, PhD José Manuel Cuevas

  33. Molecular evolution and phylogeography of potato virus Y based on the CP gene

    Article • Journal of General Virology, July 2012, Society for General Microbiology

    Professor Santiago F Elena, PhD José Manuel Cuevas

  34. Phylogeography and Molecular Evolution of Potato virus Y

    Article • PLOS One, May 2012, PLOS

    Professor Santiago F Elena, PhD José Manuel Cuevas

  35. Luria-Delbruck Estimation of Turnip Mosaic Virus Mutation Rate In Vivo

    Article • Journal of Virology, January 2012, ASM Journals

    Professor Santiago F Elena, PhD José Manuel Cuevas

  36. Transcript Profiling of Different Arabidopsis thaliana Ecotypes in Response to Tobacco etch potyvirus Infection

    Article • Frontiers in Microbiology, January 2012, Frontiers

    Professor Santiago F Elena, PhD José Manuel Cuevas

  37. Effect of Host Species on the Distribution of Mutational Fitness Effects for an RNA Virus

    Article • PLoS Genetics, November 2011, PLOS

    Professor Santiago F Elena, PhD José Manuel Cuevas

  38. Mutation rate of bacteriophage ΦX174 modified through changes in GATC sequence context

    Article • Infection Genetics and Evolution, October 2011, Elsevier

    PhD José Manuel Cuevas

  39. The Fitness Effects of Synonymous Mutations in DNA and RNA Viruses

    Article • Molecular Biology and Evolution, July 2011, Oxford University Press (OUP)

    PhD José Manuel Cuevas

  40. The Evolutionary Genetics of Emerging Plant RNA Viruses

    Article • Molecular Plant-Microbe Interactions, March 2011, Scientific Societies

    Professor Santiago F Elena, PhD José Manuel Cuevas

  41. Distribution of Fitness Effects Caused by Single-Nucleotide Substitutions in Bacteriophage f1

    Article • Genetics, June 2010, Oxford University Press (OUP)

    PhD José Manuel Cuevas

  42. The Fitness Effects of Random Mutations in Single-Stranded DNA and RNA Bacteriophages

    Article • PLoS Genetics, November 2009, PLOS

    PhD José Manuel Cuevas

  43. Point Mutation Rate of Bacteriophage ΦX174

    Article • Genetics, October 2009, Oxford University Press (OUP)

    PhD José Manuel Cuevas

  44. A genetic background with low mutational robustness is associated with increased adaptability to a novel host in an RNA virus

    Article • Journal of Evolutionary Biology, September 2009, Oxford University Press (OUP)

    PhD José Manuel Cuevas

  45. The role of positive selection in hepatitis C virus

    Article • Infection Genetics and Evolution, September 2009, Elsevier

    PhD José Manuel Cuevas

  46. Effect of Ribavirin on the Mutation Rate and Spectrum of Hepatitis C Virus In Vivo

    Article • Journal of Virology, March 2009, ASM Journals

    PhD José Manuel Cuevas

  47. Combined therapy of interferon plus ribavirin promotes multiple adaptive solutions in hepatitis C virus

    Article • Journal of Medical Virology, February 2009, Wiley

    PhD José Manuel Cuevas

  48. Enhanced adaptation of vesicular stomatitis virus in cells infected with vaccinia virus

    Article • Infection Genetics and Evolution, September 2008, Elsevier

    PhD José Manuel Cuevas

  49. Genetic Variability of Hepatitis C Virus before and after Combined Therapy of Interferon plus Ribavirin

    Article • PLOS One, August 2008, PLOS

    PhD José Manuel Cuevas

  50. Refined analysis of genetic variability parameters in hepatitis C virus and the ability to predict antiviral treatment response

    Article • Journal of Viral Hepatitis, July 2008, Wiley

    PhD José Manuel Cuevas

  51. Using evolutionary tools to refine the new hypervariable region 3 within the envelope 2 protein of hepatitis C virus

    Article • Infection Genetics and Evolution, January 2008, Elsevier

    PhD José Manuel Cuevas

  52. Hepatitis C virus and the controversial role of the interferon sensitivity determining region in the response to interferon treatment

    Article • Journal of Medical Virology, December 2007, Wiley

    PhD José Manuel Cuevas

  53. Genetic variability in hepatitis C virus and its role in antiviral treatment response

    Article • Journal of Viral Hepatitis, December 2007, Wiley

    PhD José Manuel Cuevas

  54. Contribution of insertions and deletions to the variability of hepatitis C virus populations

    Article • Journal of General Virology, August 2007, Society for General Microbiology

    PhD José Manuel Cuevas

  55. Selection for Robustness in Mutagenized RNA Viruses

    Article • PLoS Genetics, June 2007, PLOS

    PhD José Manuel Cuevas

  56. The effect of co- and superinfection on the adaptive dynamics of vesicular stomatitis virus

    Article • Infection Genetics and Evolution, January 2007, Elsevier

    PhD José Manuel Cuevas

  57. Molecular Evolution of the Plant Virus Family Bromoviridae Based on RNA3-Encoded Proteins

    Article • Journal of Molecular Evolution, October 2005, Springer Science + Business Media

    Professor Santiago F Elena, PhD José Manuel Cuevas

  58. Epistasis and the Adaptability of an RNA Virus

    Article • Genetics, May 2005, Genetics Society of America

    Professor Santiago F Elena, PhD José Manuel Cuevas

  59. Following the very initial growth of biological RNA viral clones

    Article • Journal of General Virology, February 2005, Society for General Microbiology

    PhD José Manuel Cuevas

  60. Mode of selection and experimental evolution of antiviral drugs resistance in vesicular stomatitis virus

    Article • Infection Genetics and Evolution, January 2005, Elsevier

    Professor Santiago F Elena, PhD José Manuel Cuevas

  61. Evolution of RNA virus in spatially structured heterogeneous environments

    Article • Journal of Evolutionary Biology, April 2003, Wiley

    Professor Santiago F Elena, PhD José Manuel Cuevas

  62. The Two Faces of Mutation: Extinction and Adaptation in RNA Viruses

    Article • IUBMB Life, January 2000, Wiley

    Professor Santiago F Elena, PhD José Manuel Cuevas

  63. Prevalence of 2314delG mutation in Spanish patients with Usher syndrome type II (USH2)

    Article • Ophthalmic Genetics, January 2000, Swets & Zeitlinger Publishers

    PhD José Manuel Cuevas

  64. Identification of three novel mutations in the MYO7A gene

    Article • Human Mutation, January 1999, Hindawi Publishing Corporation

    PhD José Manuel Cuevas

  65. Detection of a novel Cys628STOP mutation of the myosin VIIA gene in Usher syndrome type Ib

    Article • Molecular and Cellular Probes, December 1998, Elsevier

    PhD José Manuel Cuevas