Modelling the Evolutionary Dynamics of Viruses within Their Hosts: A Case Study Using High-Throughput Sequencing

PLoS Pathogens

Jérôme Coville¹  Josselin Montarry²  Frédéric Fabre²  Benoît Moury²  Vincent Simon³  Rachid Senoussi³ 

[1] INRA, UMR1349 IGEPP (Institute of Genetics, Environment and Plant Protection), Le Rheu, France;INRA, UR0407 Pathologie Végétale, Montfavet, France;INRA, UR546 Biostatistique et Processus Spatiaux, Montfavet, France

关键词: Leaves;    Genetic drift;    Plant genetics;    Population genetics;    Microbial genetics;    Point mutation;    Natural selection;    Viral evolution;   

DOI  :  10.1371/journal.ppat.1002654

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

Uncovering how natural selection and genetic drift shape the evolutionary dynamics of virus populations within their hosts can pave the way to a better understanding of virus emergence. Mathematical models already play a leading role in these studies and are intended to predict future emergences. Here, using high-throughput sequencing, we analyzed the within-host population dynamics of four Potato virus Y (PVY) variants differing at most by two substitutions involved in pathogenicity properties. Model selection procedures were used to compare experimental results to six hypotheses regarding competitiveness and intensity of genetic drift experienced by viruses during host plant colonization. Results indicated that the frequencies of variants were well described using Lotka-Volterra models where the competition coefficients βij exerted by variant j on variant i are equal to their fitness ratio, rj/ri. Statistical inference allowed the estimation of the effect of each mutation on fitness, revealing slight (s = −0.45%) and high (s = −13.2%) fitness costs and a negative epistasis between them. Results also indicated that only 1 to 4 infectious units initiated the population of one apical leaf. The between-host variances of the variant frequencies were described using Dirichlet-multinomial distributions whose scale parameters, closely related to the fixation index FST, were shown to vary with time. The genetic differentiation of virus populations among plants increased from 0 to 10 days post-inoculation and then decreased until 35 days. Overall, this study showed that mathematical models can accurately describe both selection and genetic drift processes shaping the evolutionary dynamics of viruses within their hosts.

【 授权许可】

CC BY