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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.

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...

Overview of Transposition and Recombination

Overview of Transposition and Recombination

Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...

Homologous Recombination

Homologous Recombination

Exon Recombination

Exon Recombination

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.
Exon shuffling follows “splice frame rules.” Each exon...

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...

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Related Experiment Video

Updated: Sep 18, 2025

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

Patterns of Recombination in Coronaviruses.

Ricardo Soares^1,2,3,4, Cristina P Vieira^1,2, Jorge Vieira^1,2

¹Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal.

International Journal of Molecular Sciences

|June 26, 2025

Summary

Recombination in coronaviruses drives adaptation and evolution. This study reveals consistent patterns across species, influenced by gene position and selection, highlighting its role in generating viral variability.

Keywords:

Coronaviridae RDP5 recombination selection

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Area of Science:

Virology
Molecular Biology
Evolutionary Biology

Background:

Coronaviruses (CoV) exhibit recombination, a key evolutionary mechanism.
Recombination contributes to adaptation in CoV species, including those causing human epidemics and pandemics.
Understanding recombination is crucial for predicting viral evolution and spread.

Purpose of the Study:

To investigate the impact of recombination inference methods and sample sizes on coronaviridae recombination analysis.
To characterize recombination patterns within and between 21 coronaviridae species.
To explore the relationship between gene position, selection, and recombination rates in coronaviruses.

Main Methods:

Analysis of recombination patterns across 21 coronaviridae species.
Utilizing various recombination inference methods and sample sizes.
Phylogenetic approaches to support recombination inferences.
Correlation analysis between gene position, recombination rates, and selection.

Main Results:

Recombination patterns show minimal variation across coronaviridae species.
A positive correlation exists between gene position and recombination rates, indicating genomic variation.
Within- and between-species recombination patterns differ, with module-type recombination prevalent except for Membrane and Nucleocapsid genes.
Module-type recombination is prevalent for the Spike gene within species.
A positive correlation between recombination and selection was observed.

Conclusions:

Recombination is a significant driver of genetic variability in coronaviruses.
Selection actively shapes intratypic recombination patterns.
Understanding these processes is vital for managing coronavirus evolution and pathogenicity.