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Related Concept Videos

Viruses with RNA Genomes01:29

Viruses with RNA Genomes

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RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
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Size and Structure of Viral Genomes01:26

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Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Viral Recombination00:57

Viral Recombination

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Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
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Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
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Genome Annotation and Assembly03:36

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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VirGenA: a reference-based assembler for variable viral genomes.

Gennady G Fedonin1, Yury S Fantin1, Alexnader V Favorov2

  • 1Department of Molecular Diagnostics, Central Research Institute for Epidemiology.

Briefings in Bioinformatics
|October 3, 2017
PubMed
Summary
This summary is machine-generated.

Understanding viral genetic diversity is key for treating infections like HIV, HBV, and HCV. VirGenA accurately identifies low-frequency viral variants and detects cross-contamination, improving diagnostic accuracy.

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Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
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Area of Science:

  • Virology
  • Genetics
  • Bioinformatics

Background:

  • Characterizing within-host viral genetic diversity is crucial for effective treatment of viral infections such as HIV, HBV, and HCV.
  • Distinguishing low-frequency variants from experimental artifacts and detecting cross-contamination are significant challenges in deep sequencing analysis.

Purpose of the Study:

  • To develop a novel viral reference-guided assembler, VirGenA, capable of separating and assembling consensus sequences for different intraspecies genetic groups within a mixture.
  • To enable the detection of low-frequency variants (<1%) and identify cross-contamination in viral samples.

Main Methods:

  • Development of VirGenA, a viral reference-guided assembler.
  • Testing VirGenA on both clinical and simulated viral sequencing data.
  • Comparison of VirGenA's performance against existing de novo assemblers.

Main Results:

  • VirGenA successfully separated mixtures of viral strains, producing long consensus sequences for components present at frequencies as low as <1%.
  • The assembler effectively detected cross-contamination by divergent genotypes.
  • VirGenA demonstrated comparable or superior performance to existing de novo assemblers on both clinical and simulated data.

Conclusions:

  • VirGenA is an effective tool for characterizing viral genetic diversity, including low-frequency variants and mixed infections.
  • The assembler aids in distinguishing true biological variants from experimental artifacts and cross-contamination.
  • VirGenA offers a valuable solution for accurate viral sequencing analysis, with its cross-platform implementation freely available.