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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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Conservative Site-specific Recombination and Phase Variation02:53

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
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Homologous Recombination02:31

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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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Exon Recombination02:32

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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Related Experiment Video

Updated: Jan 11, 2026

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings
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Geno2pheno: recombination detection for HIV-1 and HEV subtypes.

Martin Pirkl1,2, Joachim Büch1,2, Georg Friedrich3

  • 1Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany.

NAR Molecular Medicine
|November 19, 2025
PubMed
Summary
This summary is machine-generated.

A new computational tool, g2p-recco, improves the detection of human immunodeficiency virus type 1 (HIV-1) and hepatitis E virus (HEV) recombinations. This aids in selecting effective therapies and understanding viral evolution.

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Area of Science:

  • Virology
  • Computational Biology
  • Genetics

Background:

  • Antiretroviral therapy for HIV-1 has limitations, with therapy failure being a persistent challenge.
  • Recombinant viral subtypes complicate treatment efficacy, necessitating improved diagnostic methods.
  • Accurate identification of viral recombination is crucial for effective therapeutic strategies.

Purpose of the Study:

  • To introduce g2p-recco, a novel computational tool for detecting de novo and known viral recombination events.
  • To enhance the diagnosis of recombinant viral subtypes, including HIV-1 and HEV.
  • To provide a tool independent of known circulating recombinant forms (CRFs).

Main Methods:

  • Utilized a new implementation of the recco computational method for recombination detection.
  • Employed mutation calls and probable breakpoints in multiple sequence alignments to identify recombination.
  • Integrated g2p-recco into the geno2pheno web service for accessibility.
  • Applied a tuning parameter to balance mutation call and breakpoint emphasis.

Main Results:

  • Successfully detected novel and known recombinant events in HIV-1, independent of CRFs.
  • Demonstrated the tool's applicability to other viruses, such as hepatitis E virus (HEV).
  • Identified several previously unknown HEV recombinations.

Conclusions:

  • g2p-recco offers a robust method for detecting diverse viral recombinations.
  • The tool facilitates improved diagnosis, potentially leading to better therapeutic selections for HIV-1.
  • The broad applicability of g2p-recco extends its utility to other viral pathogens like HEV.