Experimental adaptation of human echovirus 11 to ultraviolet radiation leads to tolerance to disinfection and resistance to ribavirin

Ultraviolet light in the UVC range is a commonly used disinfectant to control viruses in clinical settings and water treatment. Here, we employed an experimental evolution approach to investigate the adaptation of human echovirus 11 to disinfection by UVC, and characterized the underlying phenotypic and genotypic changes. Repeated exposure to UVC lead to a reduction in the UVC inactivation rate of approximately 15%. Time-series next generation sequencing data revealed that this adaptation to UVC was accompanied by a decrease in the echovirus 11 mutation rate. The inactivation efficiency of UVC was additionally compromised by a shift from first-order to biphasic inactivation kinetics, a form of “viral persistence”. Importantly, populations with biphasic inactivation kinetics also exhibited resistance to ribavirin, a mutagenic drug. Overall, our results indicate that while the ability of echovirus 11 to adapt to UVC is limited, resistance may have relevant consequences to disinfection in both clinical and water treatment contexts.

Multi-resistance of human enterovirus to UV-C disinfection and mutagenic nucleoside analogs

Virginie Bachmann, Anna Carratala Ripolles, Tamar Kohn, Qingxia Zhong

Disinfection is an important strategy to control the environmental transmission of human viruses. Specifically, UV254 is increasingly used to disinfect from clinical items or surfaces to drinking water. RNA virus populations have high mutation rates and large population numbers that allow them to rapidly adapt to stressors. It is therefore likely that variants with enhanced resistance to disinfection may eventually emerge in a virus population. The genetic basis and mechanisms that underpin the emergence of virus resistance to disinfection remain, however, unknown. The goal of this study was to investigate the emergence of echoviruses resistant to UV254 disinfection in vitro, and to characterize the genotypic and phenotypic changes in the resistant populations as compared to the wild-type. Resistant virus populations emerged in mutation-accumulation laboratory experiments. Each experiment consisted in exposing echovirus suspensions to a UV254 fluence such that a 4.5 log10 reduction in infective viruses was achieved, and then regrowing the survivors by infecting BGM cells at a very low multiplicity of infection (MOI>0.001). Unexposed control experiments were conducted in parallel by diluting the virus suspensions instead of exposing them to UV254 prior to regrowth. We demonstrated that echovirus populations became increasingly resistant to UV254. Interestingly, a similar extent of resistance was observed in the unexposed control experiments. Fixed mutations were repeatedly identified by next generation sequencing in the 2C and 3D protein region, both involved in the genome replication. The wild-type and resistant echovirus populations exhibited an equivalent replicative fitness under standard culturing conditions. However, the UV254-resistant mutants were more resistant to ribavirin and guanidine hydrochloride. Finally, the exposed populations were able to maintain the production of infective progeny despite the effect of such chemical mutagens. Combined, these findings suggest that multi-resistance of echovirus to UV254 disinfection and treatment with mutagenic nucleotide analogs may arise in virus populations that, subjected to repeated dramatic bottlenecks, evolve towards an increased replication fidelity. The outcomes of this work show that enteric human pathogens may exhibit multi-resistance to disinfection and clinical antiviral therapies. Ultimately, the results from this work may impact future strategies to ensure adequate control of virus environmental transmission.

2016

Turnover and accumulation of genetic diversity across large time-scale cycles of isolation and connection of populations

Séverine Vuilleumier Varisco

Major climatic and geological events but also population history (secondary contacts) have generated cycles of population isolation and connection of long and short periods. Recent empirical and theoretical studies suggest that fast evolutionary processes might be triggered by such events, as commonly illustrated in ecology by the adaptive radiation of cichlid fishes (isolation and reconnection of lakes and watersheds) and in epidemiology by the fast adaptation of the influenza virus (isolation and reconnection in hosts). We test whether cyclic population isolation and connection provide the raw material (standing genetic variation) for species evolution and diversification. Our analytical results demonstrate that population isolation and connection can provide, to populations, a high excess of genetic diversity compared with what is expected at equilibrium. This excess is either cyclic (high allele turnover) or cumulates with time depending on the duration of the isolation and the connection periods and the mutation rate. We show that diversification rates of animal clades are associated with specific periods of climatic cycles in the Quaternary. We finally discuss the importance of our results for macroevolutionary patterns and for the inference of population history from genomic data

2014

Inferring the age and strength of mutations evolving under positive selection

Nicky Louise Ormond

A fundamental goal of population genetics is to determine and quantify the interplay of mutation, natural selection, genetic drift and migration in shaping allelic frequency changes that underpin evolution-ary change. In this dissertation, I present computational, empirical and experimental approaches to address this goal. In the first chapter, I develop an approximate Bayesian computation (ABC) approach that co-estimates the selection strength and age of fixed beneficial mutations in single populations, by integrating a range of existing diversity, site frequency spectrum, haplotype and linkage disequilibrium based summary statistics. This approach is then extended to models of selection on standing variation in order to co-infer the frequency at which positive selection began to act upon the mutation. In the second chapter, I apply this method to an empirical study of convergent adaptation of blanched dorsal phenotypes in two lizard species to the newly formed White Sands system of New Mexico. Estimates of the age of the beneficial mutations underpinning the evolution of cryptic coloration are younger than the related geological shift and support a model of adaptation from de novo mutation. In the third chapter, I analyze the experimental evolution of H1N1 influenza virus populations under a combined protocol of two drugs with different modes of action: oseltamivir and favipiravir. Results indicate a complex interplay of mutation, selection and genetic drift, where selective sweeps around oseltamivir resistance mutations hitchhike deleterious mutations owing to the mutagenic effect of favipiravir to fixation. This effect reduces viral fitness and ac-celerates extinction via Mullerâs ratchet, but at the risk of spreading both established and newly emerging oseltamivir resistance mutations.

EPFL2017

Multi-resistance of human enterovirus to UV-C disinfection and mutagenic nucleoside analogs

Virginie Bachmann, Anna Carratala Ripolles, Tamar Kohn, Qingxia Zhong

2016