Genetic variability plays a key role in the biology and medical treatment of RNA viruses. As an RNA virus, Hepatitis C virus (HCV) replicate as complex distributions of closely related genomes termed viral quasispecie...Genetic variability plays a key role in the biology and medical treatment of RNA viruses. As an RNA virus, Hepatitis C virus (HCV) replicate as complex distributions of closely related genomes termed viral quasispecies. The behavior of the evolving HCV quasispecies population is influenced by the ensemble of mutants that compose the viral population. One such influence is the presence of minority subpopulations, termed memory genomes, in the mutant spectra. Biologically relevant mutants have been previously observed to be present as memory genomes in RNA viral populations. For that reason, an in-depth analysis of HCV quasispecies populations is crucial for our understanding viral evolution, drug resistance and therapy outcome. Recently developed next-generation sequencing (NGS) platforms make it possible to investigate viral quasispecies at much greater detail. In order to gain insight into these matters, we have performed a Bayesian coalescent analysis of hypervariable region 1 (HVR1) sequences of a HCV quasispecies population circulating in a chronic patient, recently obtained by ultra-deep sequencing. The results of these studies revealed a mean rate of evolution of HCV HVR1 of the intra-host quasispecies population of 4.80 × 10-2 amino acid substitutions/site/year. A sharp and rapid diversification of the HCV quasispecies isolated from the patient in three different sub-populations was observed. The most abundant sequence in the quasispecies population was not found to be the center of a tight and complex network around this sequence, suggesting that the quasispecies population as a whole efficiently explore a wide sequence space. Co-evolution of relevant amino acid sites had been identified in the HVR1. This speaks of the possible roll of these residues in HVR1 to allow the virus to shift between combinations of residues to escape the immune system while retaining its structure and functions. The results of these studies highlight the importance of minority genomes in HCV population history and evolution, the mutant clouds as reservoirs of phenotypic and genetic variants for virus adaptability, as well as the roll of the mutant spectra to overcome selective constraints.展开更多
MicroRNAs (miRNAs) are small, noncoding RNA molecules that play important roles in the regulation of gene expression of the cell. Recent studies have described cytoplasmic RNA virus genome- derived miRNAs. Moreover, m...MicroRNAs (miRNAs) are small, noncoding RNA molecules that play important roles in the regulation of gene expression of the cell. Recent studies have described cytoplasmic RNA virus genome- derived miRNAs. Moreover, miRNAs have also been encountered in the reverse strand of the viral mRNA, revealing the presence of miRNAs in replication intermediaries. In order to get insight into the possible role of Hepatitis C Virus (HCV) antigenome in relation to miRNA coding, we computationally identified potential miRNAs on the antigenome of HCV reference strain H77. By utilizing a series of bioinformatics tools, we identified a miRNA present in the antigenomeof HCV H77 strain. This miRNA maps in the 5’non-translated region (5’UTR) of the HCV genome and is found to be conserved among HCV genotypes and sub-types. In silico target prediction generated 17 cellular genes. These potential targets are involved in apoptosis as well as immune response pathways, suggesting that they could play a role in the pathogenesis caused by viral infection. The results of these studies revealed the presence of a viral miRNA in the negative-sense RNA strand used as a replication template for the HCV genome, as observed for other RNA viruses.展开更多
文摘Genetic variability plays a key role in the biology and medical treatment of RNA viruses. As an RNA virus, Hepatitis C virus (HCV) replicate as complex distributions of closely related genomes termed viral quasispecies. The behavior of the evolving HCV quasispecies population is influenced by the ensemble of mutants that compose the viral population. One such influence is the presence of minority subpopulations, termed memory genomes, in the mutant spectra. Biologically relevant mutants have been previously observed to be present as memory genomes in RNA viral populations. For that reason, an in-depth analysis of HCV quasispecies populations is crucial for our understanding viral evolution, drug resistance and therapy outcome. Recently developed next-generation sequencing (NGS) platforms make it possible to investigate viral quasispecies at much greater detail. In order to gain insight into these matters, we have performed a Bayesian coalescent analysis of hypervariable region 1 (HVR1) sequences of a HCV quasispecies population circulating in a chronic patient, recently obtained by ultra-deep sequencing. The results of these studies revealed a mean rate of evolution of HCV HVR1 of the intra-host quasispecies population of 4.80 × 10-2 amino acid substitutions/site/year. A sharp and rapid diversification of the HCV quasispecies isolated from the patient in three different sub-populations was observed. The most abundant sequence in the quasispecies population was not found to be the center of a tight and complex network around this sequence, suggesting that the quasispecies population as a whole efficiently explore a wide sequence space. Co-evolution of relevant amino acid sites had been identified in the HVR1. This speaks of the possible roll of these residues in HVR1 to allow the virus to shift between combinations of residues to escape the immune system while retaining its structure and functions. The results of these studies highlight the importance of minority genomes in HCV population history and evolution, the mutant clouds as reservoirs of phenotypic and genetic variants for virus adaptability, as well as the roll of the mutant spectra to overcome selective constraints.
文摘MicroRNAs (miRNAs) are small, noncoding RNA molecules that play important roles in the regulation of gene expression of the cell. Recent studies have described cytoplasmic RNA virus genome- derived miRNAs. Moreover, miRNAs have also been encountered in the reverse strand of the viral mRNA, revealing the presence of miRNAs in replication intermediaries. In order to get insight into the possible role of Hepatitis C Virus (HCV) antigenome in relation to miRNA coding, we computationally identified potential miRNAs on the antigenome of HCV reference strain H77. By utilizing a series of bioinformatics tools, we identified a miRNA present in the antigenomeof HCV H77 strain. This miRNA maps in the 5’non-translated region (5’UTR) of the HCV genome and is found to be conserved among HCV genotypes and sub-types. In silico target prediction generated 17 cellular genes. These potential targets are involved in apoptosis as well as immune response pathways, suggesting that they could play a role in the pathogenesis caused by viral infection. The results of these studies revealed the presence of a viral miRNA in the negative-sense RNA strand used as a replication template for the HCV genome, as observed for other RNA viruses.
