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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.

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...

Conservative Site-specific Recombination and Phase Variation

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...

Homologous Recombination

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: Jun 28, 2025

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Published on: June 16, 2011

Data-driven recombination detection in viral genomes.

Tommaso Alfonsi¹, Anna Bernasconi², Matteo Chiara³

¹Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Via Ponzio 34/5, 20133, Milan, Italy.

Nature Communications

|April 17, 2024

Summary

This summary is machine-generated.

RecombinHunt accurately identifies recombinant viral genomes, including SARS-CoV-2 and monkeypox, confirming expert analyses. This data-driven method offers high accuracy and speed for detecting viral recombination events.

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Related Experiment Videos

Last Updated: Jun 28, 2025

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

Published on: June 16, 2011

Rapid, Seamless Generation of Recombinant Poxviruses using Host Range and Visual Selection

Rapid, Seamless Generation of Recombinant Poxviruses using Host Range and Visual Selection

Published on: May 24, 2020

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:

Virology
Genomics
Bioinformatics

Background:

Viral recombination is crucial for evolution and adaptation.
Over ninety SARS-CoV-2 lineages are recognized as recombinant.
Existing detection methods lack the accuracy of expert manual analysis.

Purpose of the Study:

To introduce RecombinHunt, a novel data-driven method for identifying recombinant viral genomes.
To accurately detect SARS-CoV-2 and other viral recombinants with one or two breakpoints.
To provide a reliable and efficient tool for viral recombination analysis.

Main Methods:

Developed an original data-driven computational method named RecombinHunt.
Applied RecombinHunt to identify recombinant SARS-CoV-2 genomes and lineages.
Validated RecombinHunt's performance against manual expert analyses and other state-of-the-art methods.
Tested RecombinHunt on recombinant viral genomes from the monkeypox epidemic.

Main Results:

RecombinHunt accurately identifies recombinant SARS-CoV-2 genomes and lineages with high specificity and sensitivity.
The method demonstrates high concordance with manual expert analyses.
RecombinHunt performs favorably compared to existing state-of-the-art recombination detection tools.
The tool successfully identified recombinant monkeypox viral genomes.

Conclusions:

RecombinHunt is a robust and accurate method for identifying viral recombination.
The approach offers reduced turn-around times compared to manual analysis.
RecombinHunt's effectiveness suggests its applicability to any epidemic or pandemic virus.