background more than two billion people have been exposed to hepatitis b virus (hbv) worldwide. furthermore, four hundred million of them are infected with chronic hbv infection. the predominant mutation of the precore region involves a g to a change at nucleotide1896, which creates a premature stop codon at codon 28. two mutations of a1762t and g1764a are reported as the most prevalent mutatio...

Next-generation sequencing technologies provide an unparallelled opportunity for the characterization and discovery of known and novel viruses. Because viruses are known to have the highest mutation rates when compared to eukaryotic and bacterial organisms, we assess the extent to which eleven well-known alignment algorithms (BLAST, BLAT, BWA, BWA-SW, BWA-MEM, BFAST, Bowtie2, Novoalign, GSNAP, ...

The adenovirus L4-22K protein is multifunctional and critical for different aspects of viral infection. Packaging of the viral genome into an empty capsid absolutely requires the L4-22K protein to bind to packaging sequences in cooperation with other viral proteins. Additionally, the L4-22K protein is important for the temporal switch from the early to late phase of infection by regulating both...

Because synonymous mutations do not change the amino acid sequence of a protein, they are generally considered to be selectively neutral. Empiric data suggest, however, that a significant fraction of viral mutational fitness effects may be attributable to synonymous mutation. Bias in synonymous codon usage in viruses may result from selection for translational efficiency, mutational bias, base ...

The deoxycytidine analog KP1212, and its prodrug KP1461, are prototypes of a new class of antiretroviral drugs designed to increase viral mutation rates, with the goal of eventually causing the collapse of the viral population. Here we present an extensive analysis of viral sequences from HIV-1 infected volunteers from the first "mechanism validation" phase II clinical trial of a mutagenic base...

High mutation rates typical of RNA viruses often generate a unique viral population structure consisting of a large number of genetic microvariants. In the case of viral pathogens, this can result in rapid evolution of antiviral resistance or vaccine-escape mutants. We determined a direct estimate of the mutation rate of measles virus, the next likely target for global elimination following pol...

Plant artificial micro-RNAs (amiRs) have been engineered to target viral genomes and induce their degradation. However, the exceptional evolutionary plasticity of RNA viruses threatens the durability of the resistance conferred by these amiRs. It has recently been shown that viral populations not experiencing strong selective pressure from an antiviral amiR may already contain enough genetic va...

Background: Hepatitis delta virus (HDV) is a subviral human pathogen that exploits host RNA editing activity to produce two essential forms of the sole viral protein, hepatitis delta antigen (HDAg). Editing at the amber/W site of HDV antigenomic RNA leads to the production of the large form (L-HDAg), which is required for RNA packaging. Methods: In this study, PCR-based site-directed mutagen...

Exposure to ultraviolet radiation is associated with the development of cutaneous carcinomas, and with suppression of immune responses to a variety of antigens, including those of fungal, bacterial and parasitic origin, and contact sensitizers. UV irradiation also influences viral infections. It can affect viral mutation, the photolocalization of viral exanthems, viral oncogenesis, activation o...

Duchenne muscular dystrophy (BMD) is an inherited X-link disease. The incidence of this muscle-wasting disease is 1:5000 male live births. Mutation in the gene coding for dystrophin is the main cause of BMD. Most cases of this disease succumb to respiratory and cardiac failure in 3rd to 4th decades. The slow progression of BMD and recent achievement of gene therapies make it as an appropriate c...