Search results for " Quasispecies"
showing 6 items of 26 documents
Effect of population patchiness and migration rates on the adaptation and divergence of vesicular stomatitis virus quasispecies populations
1999
The effect of migration among different isolated virus quasispecies populations on their adaptation and diversity was analysed through experimental evolution. Anin vitrocell system was employed to simulate migration of vesicular stomatitis virus between isolated homogeneous host cell populations. The results clearly demonstrated a positive correlation between the migration rate and the magnitude of the mean fitness reached by the virus quasispecies populations. The results also showed, although less clearly, that fitness differences among quasispecies decreased with the magnitude of migration. These results are in close agreement with predictions of standard population genetics theory. Thes…
PARAMETER BOUNDED ESTIMATION FOR QUASISPECIES MODELS OF MOLECULAR EVOLUTION
2006
Abstract The Quasispecies models identification for Evolutionary Dynamics is considered in a worst-case deterministic setting. These models analyze the DNA and RNA evolution or describe the population dynamics of viruses and bacteria. In this paper we identify the Fitness and the Replication Probability parameters of a genetic sequences, subject to a set of stringent constraints to have physical meaning and to guarantee positiveness. The conditional central estimate and the Uncertainty Intervals are determined. The effectiveness of the proposed procedure has been illustrated by means of simulation experiments while tests on real data are under concern.
Quasispecies dynamics and fixation of a synonymous mutation in hantavirus transmission.
2008
RNA-dependent RNA polymerases, the key enzymes in replication of RNA viruses, have a low fidelity; thus, these viruses replicate as a swarm of mutants termed viral quasispecies. Constant generation of new mutations allows RNA viruses to adapt swiftly to a novel environment through selection of both pre-existing and de novo-generated genetic variants. Here, quasispecies dynamics were studied in vivo in controlled hantavirus transmission from experimentally infected to naïve rodents through infested cage bedding. An elementary step of virus microevolution was apparent, as one synonymous mutation (A759G) repeatedly became fixed in the viral RNA quasispecies populations in the recipient animals.
Quasispecies dynamics and molecular evolution of human norovirus capsid P region during chronic infection.
2009
In this novel study, we have for the first time identified evolutionarily conserved capsid residues in an individual chronically infected with norovirus (GGII.3). From 2000 to 2003, a total of 147 P1-1 and P2 capsid sequences were sequenced and investigated for evolutionarily conserved and functionally important residues by the evolutionary trace (ET) algorithm. The ET algorithm revealed more absolutely conserved residues (ACR) in the P1-1 domain (47/53, 88 %) as compared with the P2 domain (86/133, 64 %). The capsid P1-1 and P2 domains evolved in time-dependent manner, with a distinct break point observed between autumn/winter of year 2000 (isolates P1, P3 and P5) and spring to autumn of y…
In-Depth Characterization of Viral Isolates from Plasma and Cells Compared with Plasma Circulating Quasispecies in Early HIV-1 Infection
2012
Background The use of in vitro models to unravel the phenotypic characteristics of circulating viral variants is key to understanding HIV-1 pathogenesis but limited by the availability of primary viral isolates from biological samples. However, overall in vivo genetic variability of HIV-1 within a subject may not be reflected in the viable viral population obtained after isolation. Although several studies have tried to determine whether viral populations expanded in vitro are representative of in vivo findings, the answer remains unclear due to the reduced number of clonal sequences analyzed or samples compared. In order to overcome previous experimental limitations, here we applied Deep P…
Is the Quasispecies Concept Relevant to RNA Viruses?
2002
The study of RNA virus evolution has blossomed over the last 20 years. Despite the emergence of this new discipline, there has been little active debate over perhaps the most fundamental question of all. Do RNA viruses evolve in a manner that is qualitatively different from other life forms? For