The dark side of evolution: the deleterious mutational landscape of RNA viruses

Descripción del proyecto

Mutaciones malignas en la evolución de los virus ARN

Las mutaciones malignas no se han estudiado lo suficiente en comparación con las mutaciones beneficiosas, dado que no ha resultado técnicamente viable secuenciar cada una de las de tipo maligno. Recientemente, las técnicas de secuenciación de próxima generación han mostrado que una parte significativa de la diversidad genética vírica es consecuencia de mutaciones malignas. El proyecto financiado con fondos europeos RNAVirFitness investiga la distribución de los efectos de adecuación en una amplia variedad de virus ARN, con representantes de cada clase de los principales patógenos humanos, tanto «in vivo» como «in vitro». El proyecto analizará la manera en que la acumulación de mutaciones malignas puede dar lugar a la extinción de la población vírica, y cómo se puede utilizar esta información en una nueva estrategia para hacer frente a las epidemias víricas. Además de la contribución a la biología evolutiva, los resultados se pueden aprovechar para diseñar nuevas cepas de vacunas y para desarrollar opciones terapéuticas antivíricas de amplio espectro.

Objetivo

Mutations are fundamental drivers of evolution. Characterizing how mutations affect fitness is critical across diverse fields: from pathogen biology, to human genetic diseases, and models of population extinction. RNA viruses, notorious for their high mutation rates and rapid generation times, are ideal models for studying the effects of mutations. To date, deleterious mutations (i.e. mutations with a fitness cost) have been understudied as compared to beneficial mutations, mainly since it has been technically unfeasible to sequence each single rare deleterious mutation. Using novel next generation sequencing (NGS) techniques, we and others have recently overcome this gap, and shown that an appreciable proportion of viral genetic diversity is a consequence of a multitude of rare deleterious mutations. Here, we suggest investigating the distribution of fitness effects (DFE) across a diverse array of RNA viruses, spanning representatives of each class of major human pathogens, both in vivo (in patients) and in vitro (in cell culture). Next, we will focus on genetic linkage and context-dependent fitness effects of mutations. We postulate that over- and under-represented sequence contexts may represent signatures of host anti-viral activity. Finally, we will investigate how the DFE changes following an environmental perturbation (physical and metabolic changes, tissue type, and sex of the host). We will explore how the accumulation of deleterious mutations following rapid perturbations may lead to the extinction of the viral population, and how this can be used as a novel strategy to tackle viral epidemics. To this end we will integrate state-of-the-art NGS, population genetics modelling, and reverse genetics validation. Beyond their contribution to evolutionary biology, we anticipate that our results may be harnessed for the design of safe and effective attenuated vaccine strains, and the development of broad-spectrum antiviral therapeutic strategies.