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Related Concept Videos

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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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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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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Retrovirus Life Cycles01:10

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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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Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
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Updated: Nov 6, 2025

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

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VIRUSBreakend: Viral Integration Recognition Using Single Breakends.

Daniel L Cameron1,2,3, Nina Jacobs4, Paul Roepman4

  • 1Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.

Bioinformatics (Oxford, England)
|May 11, 2021
PubMed
Summary
This summary is machine-generated.

VIRUSBreakend is a new high-speed tool that detects viral DNA and genomic integration with high sensitivity. It overcomes limitations of existing software, enabling detection of viruses like HPV and HBV in cancer genomes.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Virology

Background:

  • Viral integration into host DNA can cause genetic damage and gene disruption.
  • Advances in whole genome sequencing enable viral detection, but existing tools face limitations.
  • These limitations include high computational costs, narrow virus detection range, and suboptimal precision/sensitivity.

Purpose of the Study:

  • To introduce VIRUSBreakend, a novel, high-speed computational tool for detecting viral DNA presence and genomic integration.
  • To address the limitations of existing software in terms of speed, virus detection breadth, precision, and sensitivity.

Main Methods:

  • VIRUSBreakend employs a novel virus-centric variant calling and assembly approach using single breakends.
  • It is integrated into the Genomic Rearrangement IDentification Software Suite (GRIDSS).

Main Results:

  • VIRUSBreakend achieves high sensitivity and a near-zero false discovery rate in identifying viral integrations.
  • The tool successfully detects viral integrations in challenging genomic regions like centromeres and telomeres.
  • Application to a metastatic cancer cohort demonstrated reliable detection of clinically relevant viruses (HPV, HBV, MCPyV, EBV, HHV-8).

Conclusions:

  • VIRUSBreakend offers a significant advancement in detecting viral DNA and genomic integration.
  • Its high speed, sensitivity, and broad detection capabilities make it a valuable tool for cancer genomics research.
  • The software is freely available, promoting wider adoption and research in the field.