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Viral Structure

Viral Structure

Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.

What are Viruses?

What are Viruses?

Viral Mutations

Viral Mutations

A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...

Viral Recombination

Viral Recombination

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.

Retrovirus Life Cycles

Retrovirus Life Cycles

Retroviruses have a single-stranded RNA genome that undergoes a special form of replication. Once the retrovirus has entered the host cell, an enzyme called reverse transcriptase synthesizes double-stranded DNA from the retroviral RNA genome. This DNA copy of the genome is then integrated into the host’s genome inside the nucleus via an enzyme called integrase. Consequently, the retroviral genome is transcribed into RNA whenever the host’s genome is transcribed, allowing the...

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Updated: May 24, 2025

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

Published on: July 18, 2013

Virusplot: a web server for viral integration analysis and visualization.

Erqiang Hu^1,2,3, Jianhong An^1,2,3, Adam J Gersten^1,4

¹Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States.

Frontiers in Oncology

|March 6, 2025

Summary

This summary is machine-generated.

Viral DNA integration into the human genome drives cancer by causing genomic instability. We developed virusPlot, a web tool for analyzing and visualizing these viral integration sites, simplifying complex data for researchers.

Keywords:

bioinformatics tool computational biology genomic visualization host-virus interaction hotspot analysis viral integration

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Last Updated: May 24, 2025

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

Published on: July 18, 2013

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

Area of Science:

Genomics and Bioinformatics
Oncology and Virology

Background:

Viral DNA integration into the human genome is a key factor in cancer development, leading to genomic instability and altered gene expression.
Existing computational tools for analyzing viral integration are limited, especially web-based applications for visualization and interpretation.

Purpose of the Study:

To develop and present virusPlot, a novel web server designed for the analysis and visualization of viral DNA integration into host genomes.
To provide researchers with an intuitive and user-friendly tool to simplify the interpretation of complex viral integration patterns.

Main Methods:

Developed virusPlot as an interactive web platform using shinyapp.
Implemented modules for automatic retrieval and annotation of viral genome sequences.
Integrated visualization of viral and host genome integration sites, read counts, and analysis of integration hotspots using Fisher's exact test.

Main Results:

VirusPlot successfully processes and visualizes viral integration data, linking viral and host genome integration sites.
The tool facilitates the identification of integration patterns and hotspots.
Provides an interactive graphical representation for easier interpretation of integration data.

Conclusions:

VirusPlot addresses the need for specialized computational tools in viral integration analysis.
The web server offers an efficient and user-friendly solution for researchers studying virus-host genome interactions in cancer pathogenesis.
Enhances the understanding of viral integration mechanisms and their role in cancer.