scholarly journals Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 96 ◽  
Author(s):  
Haiyin Chen-Harris ◽  
Monica K Borucki ◽  
Clinton Torres ◽  
Tom R Slezak ◽  
Jonathan E Allen
Keyword(s):  
Mutant Spectrum

scholarly journals Extinction of West Nile Virus by Favipiravir through Lethal Mutagenesis

2017 ◽  
Vol 61 (11) ◽  
Author(s):  
Estela Escribano-Romero ◽  
Nereida Jiménez de Oya ◽  
Esteban Domingo ◽  
Juan Carlos Saiz
Keyword(s):  
West Nile Virus ◽  
Mutation Frequency ◽  
Ebola Virus ◽  
Rna Viruses ◽  
Lethal Dose ◽  
Antiviral Agent ◽  
West Nile ◽  
Lethal Mutagenesis ◽  
Mutant Spectrum

ABSTRACT Favipiravir is an antiviral agent effective against several RNA viruses. The drug has been shown to protect mice against experimental infection with a lethal dose of West Nile virus (WNV), a mosquito-borne flavivirus responsible for outbreaks of meningitis and encephalitis for which no antiviral therapy has been licensed; however, the mechanism of action of the drug is still not well understood. Here, we describe the potent in vitro antiviral activity of favipiravir against WNV, showing that it decreases virus-specific infectivity and drives the virus to extinction. Two passages of WNV in the presence of 1 mM favipiravir—a concentration that is more than 10-fold lower than its 50% cytotoxic concentration (CC50)—resulted in a significant increase in mutation frequency in the mutant spectrum and in a bias toward A→G and G→A transitions relative to the population passaged in the absence of the drug. These data, together with the fact that the drug is already licensed in Japan against influenza virus and in a clinical trial against Ebola virus, point to favipiravir as a promising antiviral agent to fight medically relevant flaviviral infections, such as that caused by WNV.

scholarly journals Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum

2015 ◽  
Vol 31 (13) ◽  
pp. 2141-2150 ◽  
Author(s):  
Ofer Isakov ◽  
Antonio V. Bordería ◽  
David Golan ◽  
Amir Hamenahem ◽  
Gershon Celniker ◽  
...  
Keyword(s):  
Viral Infection ◽  
Deep Sequencing ◽  
Sequencing Analysis ◽  
Detailed Characterization ◽  
Viral Mutant ◽  
Mutant Spectrum ◽  
Deep Sequencing Analysis

scholarly journals Internal Disequilibria and Phenotypic Diversification during Replication of Hepatitis C Virus in a Noncoevolving Cellular Environment

2017 ◽  
Vol 91 (10) ◽  
Author(s):  
Elena Moreno ◽  
Isabel Gallego ◽  
Josep Gregori ◽  
Adriana Lucía-Sanz ◽  
María Eugenia Soria ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Virus Evolution ◽  
Progeny Production ◽  
Human Hepatoma Cells ◽  
Cellular Environment ◽  
Mutant Spectrum ◽  
Phenotypic Diversification ◽  
Population Equilibrium

ABSTRACT Viral quasispecies evolution upon long-term virus replication in a noncoevolving cellular environment raises relevant general issues, such as the attainment of population equilibrium, compliance with the molecular-clock hypothesis, or stability of the phenotypic profile. Here, we evaluate the adaptation, mutant spectrum dynamics, and phenotypic diversification of hepatitis C virus (HCV) in the course of 200 passages in human hepatoma cells in an experimental design that precluded coevolution of the cells with the virus. Adaptation to the cells was evidenced by increase in progeny production. The rate of accumulation of mutations in the genomic consensus sequence deviated slightly from linearity, and mutant spectrum analyses revealed a complex dynamic of mutational waves, which was sustained beyond passage 100. The virus underwent several phenotypic changes, some of which impacted the virus-host relationship, such as enhanced cell killing, a shift toward higher virion density, and increased shutoff of host cell protein synthesis. Fluctuations in progeny production and failure to reach population equilibrium at the genomic level suggest internal instabilities that anticipate an unpredictable HCV evolution in the complex liver environment. IMPORTANCE Long-term virus evolution in an unperturbed cellular environment can reveal features of virus evolution that cannot be explained by comparing natural viral isolates. In the present study, we investigate genetic and phenotypic changes that occur upon prolonged passage of hepatitis C virus (HCV) in human hepatoma cells in an experimental design in which host cell evolutionary change is prevented. Despite replication in a noncoevolving cellular environment, the virus exhibited internal population disequilibria that did not decline with increased adaptation to the host cells. The diversification of phenotypic traits suggests that disequilibria inherent to viral populations may provide a selective advantage to viruses that can be fully exploited in changing environments.

Ac/Ds transposon mutagenesis in Arabidopsis thaliana: mutant spectrum and frequency of Ds insertion mutants

1995 ◽  
Vol 247 (5) ◽  
pp. 646-652 ◽  
Author(s):  
Thomas Altmann ◽  
Gisela Felix ◽  
Alison Jessop ◽  
Annette Kauschmann ◽  
Ursula Uwer ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transposon Mutagenesis ◽  
Mutant Spectrum ◽  
Insertion Mutants

scholarly journals Role of the mutant spectrum in adaptation and replication of West Nile virus

2007 ◽  
Vol 88 (3) ◽  
pp. 865-874 ◽  
Author(s):  
Alexander T. Ciota ◽  
Kiet A. Ngo ◽  
Amy O. Lovelace ◽  
Anne F. Payne ◽  
Yangsheng Zhou ◽  
...  
Keyword(s):  
West Nile Virus ◽  
Reverse Genetics ◽  
Viral Fitness ◽  
West Nile ◽  
Mosquito Cells ◽  
The Usa ◽  
Mutant Spectrum ◽  
Vertebrate Hosts ◽  
Adaptive Constraints

West Nile virus (WNV) has successfully spread throughout the USA, Canada, Mexico, the Caribbean and parts of Central and South America since its 1999 introduction into North America. Despite infecting a broad range of both mosquito and avian species, the virus remains highly genetically conserved. This lack of evolutionary change over space and time is common with many arboviruses and is frequently attributed to the adaptive constraints resulting from the virus cycling between vertebrate hosts and invertebrate vectors. WNV, like most RNA viruses studied thus far, has been shown in nature to exist as a highly genetically diverse population of genotypes. Few studies have directly evaluated the role of these mutant spectra in viral fitness and adaptation. Using clonal analysis and reverse genetics experiments, this study evaluated genotype diversity and the importance of consensus change in producing the adaptive phenotype of WNV following sequential mosquito cell passage. The results indicated that increases in the replicative ability of WNV in mosquito cells correlate with increases in the size of the mutant spectrum, and that consensus change is not solely responsible for alterations in viral fitness and adaptation of WNV. These data provide evidence of the importance of quasispecies dynamics in the adaptation of a flavivirus to new and changing environments and hosts, with little evidence of significant genetic change.

scholarly journals Broad and Dynamic Diversification of Infectious Hepatitis C Virus in a Cell Culture Environment

2019 ◽  
Vol 94 (6) ◽  
Author(s):  
Isabel Gallego ◽  
María Eugenia Soria ◽  
Carlos García-Crespo ◽  
Qian Chen ◽  
Patricia Martínez-Barragán ◽  
...  
Keyword(s):  
Cell Culture ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Consensus Sequence ◽  
Large Population ◽  
Viral Fitness ◽  
Initial Population ◽  
Constant Environment ◽  
Mouth Disease Virus ◽  
Mutant Spectrum

ABSTRACT Previous studies documented that long-term hepatitis C virus (HCV) replication in human hepatoma Huh-7.5 cells resulted in viral fitness gain, expansion of the mutant spectrum, and several phenotypic alterations. In the present work, we show that mutational waves (changes in frequency of individual mutations) occurred continuously and became more prominent as the virus gained fitness. They were accompanied by an increasing proportion of heterogeneous genomic sites that affected 1 position in the initial HCV population and 19 and 69 positions at passages 100 and 200, respectively. Analysis of biological clones of HCV showed that these dynamic events affected infectious genomes, since part of the fluctuating mutations became incorporated into viable genomes. While 17 mutations were scored in 3 biological clones isolated from the initial population, the number reached 72 in 3 biological clones from the population at passage 200. Biological clones differed in their responses to antiviral inhibitors, indicating a phenotypic impact of viral dynamics. Thus, HCV adaptation to a specific constant environment (cell culture without external influences) broadens the mutant repertoire and does not focus the population toward a limited number of dominant genomes. A retrospective examination of mutant spectra of foot-and-mouth disease virus passaged in cell cultures suggests a parallel behavior here described for HCV. We propose that virus diversification in a constant environment has its basis in the availability of multiple alternative mutational pathways for fitness gain. This mechanism of broad diversification should also apply to other replicative systems characterized by high mutation rates and large population sizes. IMPORTANCE The study shows that extensive replication of an RNA virus in a constant biological environment does not limit exploration of sequence space and adaptive options. There was no convergence toward a restricted set of adapted genomes. Mutational waves and mutant spectrum broadening affected infectious genomes. Therefore, profound modifications of mutant spectrum composition and consensus sequence diversification are not exclusively dependent on environmental alterations or the intervention of population bottlenecks.

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