Mutation rates

Mutation is the ultimate source of genetic variation and, as such, a key factor explaining the high variability and fast evolution of RNA viruses.

i. We have recently shown that lab estimated viral mutation rates correlate with evolution rates measured in the field over time spans of decades (2012).

ii. We have recently published an extensive review of viral mutation rate estimates (2010) (see associated on-line resource).

iii. We showed the single stranded ssDNA phage phiX174 is adversely affected by nucleoside analogue mutagenesis and evolves resistance mechanisms despite its genome does not encode a DNA polymerase (2012).

iv. We have exploited he well-known E.coli methyl-directed mistmatch repair system to engineer ssDNA phages with altered mutation rates (2011).

v. Using a large dataset of molecular clone sequences from a local hepatitis C virus outbreak, we showed that the current ribavirin plus interferon treatment increases the mutation rate of the virus by aprox. threefold, and thus that viral mutagenesis might contribute to the therapeutic effect of this treatment (2009).

vi. We measured the mutation rate of Chrysanthemum chlorotic mottle viroid (CChMVd) and shown that it is the highest described for any biological entity (2009).

vii. We measured the mutation rate of the  bacteriophage phiX174 using the Luria-Delbrück fluctuation test (2009). Our estimate confirmed Drake's rule, which states that DNA-based mircoorganisms (DNA viruses, bacteria, unicellular eukaryotes) show a constant genomic mutation rate of ~0.003 substitutions per genome per round of copying, despite large variations in lifestyle and genome complexity.

viii. Estimation of the mutation rate of VSV using the Luria-Delbrück fluctuation test (2005).

ix. Upper-limit estimation of the mutation rate of Tobacco etch virus (2009).

x. Fitness costs of replication fidelity in RNA viruses (2005, 2007).

xi. Selection fails to optimize mutation rates in digital organisms (2008).
    

Robustness

The ability of organisms to tolerate mutations (mutational or genetic robustness) determines the strength of natural selection and as such, plays an important role in evolution.

i. Using a series of VSV single-nucleotide mutants obtained by site-directed mutagenesis, we were the first to directly characterize the distribution of mutational fitness effects in an RNA virus (2004). This work established that RNA viruses show remarkably low robustness, roughly 40% of random point mutations being lethal in the case of VSV.

ii. The above results have been extended to other RNA viruses and single-stranded DNA viruses (2007-2010). Recently, I  published a review on the use of site-directed mutagenesis as a valuable tool for characterizing the fitness effects of random mutations in viruses (2010).

iii. We have also characterized the fitness effects of synonymous substitutions in RNA viruses and found that they can contribute significantly to shaping genetic variability and evolution. The effects of synonymous substitutions are much weaker in DNA viruses (2011).

iv. Due to their high mutation rates and low robustness, RNA viruses are a good target for lethal mutagenesis. We developed a population genetics theory of lethal mutagenesis in viruses, in collaboration with Prof. Jim Bull and Dr. Claus Wilke (University of Texas) (2007).

v. We demonstrated that increased robustness offers a selective advantage in viral populations subjected to chemical mutagenesis (2007). This work also provided support for a prediction of the quasispecies theory known as " the survival of the flattest ".

vi. The relationship between robustness and evolvability remains controversial.  We showed that, in VSV, increased robustness appears to hamper adaptation (2009).

vii. We showed that selection for thermostability can lead to the emergence of mutational robustness in the bacteriophage Qbeta (2010).

viii. We have also studied robustness in viroids. Using RNA folding algorithms, we predicted the  effect of all possible single substitutions on the secondary structure of 29 viroid species (2006). We also developed a one-step site-directed mutagenesis lab protocol for viroids which facilitates the creation of mutant collections (2007).


Epistasis

Epistasis (the interaction between genes or loci) is central to several population-genetic theories, including those seeking to explain sexual reproduction, ploidy, or speciation. More recently, systems biology has opened new avenues for the study of epistasis.

i. In a collaboration with Prof. Santiago Elena (CSIC), we proposed the existence of a general correlation between  epistasis and genome complexity, and supported it using experimental data from viruses, prokaryotes, unicellular eukaryotes and higher eukaryotes (2006).

ii. In a collaboration with Dr. Miguel R. Nebot (University of Valencia), we developed a simple gene network model for explaining the above correlation between epistasis and genome complexity (2008).

iii. We characterized the distribution of epistasis coefficients between random pairs of mutations obtained by site-directed mutagenesis in VSV (2004).

iv. We studied epistasis in viroids using RNA folding algorithms. In this work, we provided evidence for the hypothesis that epistasis and robustness are correlated traits (2006).

v. Selection and epistasis coefficients for an essential regulatory RNA secondary structure of the Rous sarcoma virus (2006).


Other studies 

i. Fitness-virulence relationship in the vesicular stomatitis virus (2012).

ii. Assessment of the evolvability of RNA and DNA viruses in the laboratory: RNA viruses evolve faster but the difference is less  than expected from differences in mutation rates (2011).

iii.  Selection acting at the level of RNA struture can constrain the evolution of HIV-1 at other levels, such as the emergence of drug resistance or immune escape (2011).

iv. Co-infection with Vaccinia virus enhances VSV adaptability (2008)

v. Development of a least-squares statistical test for assessing the confidence of distance-based phylogenetic trees (2005)

vi. Effect of ribavirin/interferon treatment on VSV fitness and evolvability (2005)

vii. Assessment of the relative importance of compensatory evolution and reversion in VSV experimental populations undergoing fitness recovery (2005)

viii. Identification of trade-offs between fitness-related traits in VSV in cell cultures (2005)

ix. The role of natural selection in the organ compartmentalization of HIV-1 within patients (2004)

x. Study of the role played by gene duplications in the evolution of novel functions (2001)

xi. Effects of transmission mode and genetic bottlenecking on the fitness of VSV in the laboratory (2001)