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Related Concept Videos

Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

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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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Viruses with RNA Genomes01:29

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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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Related Experiment Video

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Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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Towards quantitative viromics for both double-stranded and single-stranded DNA viruses.

Simon Roux1, Natalie E Solonenko1, Vinh T Dang2

  • 1Department of Microbiology, The Ohio State University , Columbus , OH , United States.

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|December 23, 2016
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This study introduces a new method to accurately quantify single-stranded DNA (ssDNA) viruses in environmental samples. The findings reveal the true abundance of these viruses, previously underestimated in aquatic ecosystems.

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Environmental virologyViral metagenomicsssDNA viruses

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Area of Science:

  • Virology
  • Environmental Microbiology
  • Genomics

Background:

  • Viruses significantly impact microbial populations and ecosystem functions.
  • Quantitative analysis of viral communities is limited, especially for non-double-stranded DNA (dsDNA) viruses like single-stranded DNA (ssDNA) viruses.
  • Existing sequencing methods introduce amplification biases, hindering accurate quantification of ssDNA viruses in viromes.

Purpose of the Study:

  • To develop and evaluate a sequencing library preparation protocol for the accurate quantification of both ssDNA and dsDNA viruses.
  • To provide the first quantitative estimates of ssDNA virus abundance in aquatic environments.

Main Methods:

  • Designed mock viral communities containing both ssDNA and dsDNA viruses.
  • Tested a novel library preparation approach incorporating an Adaptase step before Linker Amplification.
  • Applied the optimized protocol to analyze viral communities from freshwater and marine samples.

Main Results:

  • The Adaptase plus Linker Amplification protocol demonstrated quantitative amplification of both ssDNA and dsDNA templates (±1.8-fold accuracy).
  • Existing library preparation methods showed significant biases against or enrichment of ssDNA templates.
  • ssDNA viruses constitute a minor fraction (<5%) of overall DNA virus communities in aquatic systems.
  • Specific ssDNA viruses, including Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and Microviridae bacteriophages, can be highly abundant.

Conclusions:

  • The study provides empirical validation for a new, quantitative virome library preparation protocol.
  • This research offers the first quantitative estimates of ssDNA virus prevalence in aquatic ecosystems.
  • The findings improve our understanding of viral diversity and ecological roles in aquatic environments.