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Related Concept Videos

Viral Recombination00:57

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.
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

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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Related Experiment Video

Updated: Jun 30, 2026

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
09:31

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

Published on: March 22, 2016

An exploratory algorithm to identify intra-host recombinant viral sequences.

Marco Salemi1, Rebecca R Gray, Maureen M Goodenow

  • 1Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, College of Medicine, 1376 Mowry Road, P.O. Box 106633, Gainesville, FL 32610, USA. salemi@pathology.ufl.edu

Molecular Phylogenetics and Evolution
|September 20, 2008
PubMed
Summary
This summary is machine-generated.

Detecting viral recombination within hosts is challenging. This study introduces a new method to identify intra-host recombinants, revealing that HIV-1 recombination is more common than previously believed.

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Area of Science:

  • Virology
  • Computational Biology
  • Genetics

Background:

  • Recombination generates mosaic genomes, challenging traditional phylogenetic analyses that assume single-tree evolution.
  • Detecting recombination between diverse sequences (e.g., HIV-1 subtypes) is feasible, but identifying recombinants within closely related viral populations (intra-host) is more difficult.

Purpose of the Study:

  • To develop a simple algorithmic procedure for detecting intra-host recombinants.
  • To assess the frequency of intra-host recombination in human immunodeficiency virus type 1 (HIV-1).

Main Methods:

  • Utilized split-decomposition networks for identifying potential recombinants.
  • Implemented a robust statistical test to confirm recombination events.
  • Applied the algorithm to published HIV-1 env sequence datasets.

Main Results:

  • The new algorithm successfully detected intra-host recombinants.
  • Intra-host recombination was significantly underestimated in previous studies.
  • Up to one-third of longitudinally sampled HIV-1 env sequences from individuals could be recombinant.

Conclusions:

  • The developed procedure is a valuable tool for detecting recombinant sequences prior to phylogenetic analysis.
  • In vivo HIV-1 recombination occurs more frequently and is more significant than previously recognized.