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Related Concept Videos

Introduction to Virus01:28

Introduction to Virus

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Viruses are unique biological entities that blur the boundary between living and non-living systems. Although they lack cellular structure and metabolic processes, they can exhibit characteristics of life when infecting a host. Their defining feature is a nucleic acid core, composed of either DNA or RNA, encapsulated within a protein coat called a capsid. This simple structure allows them to invade host cells and use their machinery for replication efficiently.Viral Structure and...
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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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Archaeal viruses play a crucial role in the ecosystems of extremophilic archaea, particularly those belonging to the phyla Euryarchaeota and Crenarchaeota. By shaping host evolution and facilitating gene transfer, these viruses influence microbial communities and contribute to genetic diversity in extreme environments. The archaea they infect thrive in acidic hot springs and hydrothermal vents characterized by high temperatures and low pH. Archaeal viruses exhibit remarkable structural...
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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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The human body harbors a vast and diverse viral community known as the human virome. The virome includes bacteriophages that infect bacteria, and eukaryotic viruses that infect human cells. Transient dietary and environmental viruses also contribute to this dynamic ecosystem. Estimates suggest the human body may contain on the order of 10¹³ viral particles, though abundance varies widely by body site and detection method.Comprehensive characterization of the virome has become possible...
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Related Experiment Video

Updated: May 4, 2026

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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vAMPirus: A versatile amplicon processing and analysis program for studying viruses.

Alex J Veglia1,2,3, Ramón E Rivera-Vicéns3,4,5, Carsten G B Grupstra1,6

  • 1BioSciences Department, Rice University, Houston, Texas, USA.

Molecular Ecology Resources
|May 22, 2024
PubMed
Summary

vAMPirus is a new tool for analyzing viral communities using amplicon sequencing. It provides reproducible insights into virus diversity and population dynamics in environmental samples.

Keywords:
DNARNAamino acidamplicon sequencingbioinformaticsdiversityvirus

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Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
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Area of Science:

  • Environmental Virology
  • Bioinformatics
  • Computational Biology

Background:

  • Amplicon sequencing is a powerful method for studying environmental viral communities.
  • Analyzing complex viral sequence data requires robust and reproducible bioinformatics tools.

Purpose of the Study:

  • To introduce vAMPirus, a versatile program for analyzing DNA and RNA virus amplicon sequencing data.
  • To provide researchers with a user-friendly, comprehensive, and reproducible workflow for viral community analysis.

Main Methods:

  • vAMPirus integrates 16 open-source tools for nucleotide- and amino acid-based analyses.
  • The workflow is streamlined using Nextflow for scalability and standardization.
  • Optional approaches are included to enhance signal-to-noise ratio in data.

Main Results:

  • vAMPirus generates sequence abundance, taxonomic classifications, phylogenies, and diversity metrics.
  • The framework was validated by recapitulating findings from two published DNA virus datasets.
  • A case study demonstrated its application in exploring coral reef-associated RNA virus diversity.

Conclusions:

  • vAMPirus offers a streamlined, adaptable, and reproducible framework for virus amplicon sequencing analysis.
  • The tool aids in revealing patterns of virus diversity and population dynamics.
  • It promotes comparability and reproducibility in viral ecology studies.