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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...
Viral Mutations00:36

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 for adaptive...
Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

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...
Retrovirus Life Cycles01:10

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 retrovirus to...
Homologous Recombination02:31

Homologous Recombination

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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Related Experiment Video

Updated: May 12, 2026

Molecular Evolution of the Tre Recombinase
12:02

Molecular Evolution of the Tre Recombinase

Published on: May 29, 2008

Modeling sequence evolution in HIV-1 infection with recombination.

Elena E Giorgi1, Bette T Korber, Alan S Perelson

  • 1Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.

Journal of Theoretical Biology
|April 10, 2013
PubMed
Summary

Even with complex models of HIV-1 evolution, genetic distance increases linearly over time. Recombination does not alter this linear growth, suggesting robust evolutionary dynamics.

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Interview: HIV-1 Proviral DNA Excision Using an Evolved Recombinase

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Area of Science:

  • Virology
  • Evolutionary Biology
  • Mathematical Modeling

Background:

  • Previous simplified models suggested linear growth of genetic distance in early HIV-1 evolution under neutral conditions.
  • Understanding viral evolution is crucial for developing effective treatments and vaccines.

Purpose of the Study:

  • To develop and analyze a more realistic, age-dependent mathematical model of HIV-1 infection and replication.
  • To determine if the linear growth of mean Hamming distance holds in a complex model and with recombination.

Main Methods:

  • Developed a continuous-time, age-dependent mathematical model for viral infection and replication.
  • Performed simulations to analyze the growth of mean Hamming distance (HD) over time.
  • Introduced recombination into the model to assess its impact on HD.

Main Results:

  • Simulations confirmed that mean Hamming distance grows linearly with time, even in the complex age-dependent model.
  • The linear growth of mean HD remained consistent even when recombination was introduced.
  • Ignoring recombination resulted in overly conservative confidence intervals for mean HD.

Conclusions:

  • The linear growth of mean Hamming distance is a robust feature of early HIV-1 evolution, persisting in more complex models.
  • Recombination does not change the fundamental linear trend of genetic divergence.
  • Current models may underestimate the variability in genetic distance if recombination is ignored.