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We demonstrate the performance of our novel mutation distribution analysis of populations (MDAP) microarray by characterizing the mutant spectrum of a poliovirus population subjected to a mutagenic drug.
To determine whether the mutant spectrum of V3A included genomes with the same mutations found in the other lineages, the P2 P3 coding region of virus isolated from 5 individual plaques derived from population V3A at passage 1 was sequenced.
For many purposes it is important to analyze phylogenetically the relationship among different genomes from the same mutant spectrum of a viral quasispecies.
The mutation profile in the components of the mutant spectrum of each population analyzed indicated that a specific pattern of mutations was associated with each mutagen.
In good agreement with this expectation, all substitutions represented at a frequency ≥ 0.2 in the mutant spectrum of a given population appeared also as double peaks in the chromatogram of the consensus sequence of the same population.
Our results show that virus replication under mutagenic conditions can lead to the simultaneous presence in the mutant spectrum of multiple mutations conferring different advantages in the presence of the mutagen.
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Minority genomes in the mutant spectra of viral quasispecies may differ in relative fitness.
Our results suggest a model for the evolution of virulence in viruses based on internal interactions within mutant spectra of viral quasispecies.
New generation sequencing is greatly expanding the capacity to examine the composition of mutant spectra of viral quasispecies in infected cells and host organisms.
Analysis of the mutant spectra of virus populations selected with different concentrations of antibody in infections in liquid culture medium has documented a dominance of the high fitness counterpart in the selected population.
However, possible alterations of phylogenetic relationships among components of the mutant spectra of mutagenized quasispecies have not been studied.
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