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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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Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
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Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

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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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Viral Mutations00:36

Viral Mutations

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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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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Homologous Recombination02:31

Homologous Recombination

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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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Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization
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Conserved recombination patterns across coronavirus subgenera.

Arné de Klerk1, Phillip Swanepoel1, Rentia Lourens2

  • 1Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa.

Virus Evolution
|July 11, 2022
PubMed
Summary
This summary is machine-generated.

Coronavirus recombination patterns are non-random, influenced by sequence features and selection. Conserved recombination hotspots are linked to transcriptional regulatory sequences and gene structures, impacting viral evolution.

Keywords:
CoronavirusEvolutionPhylogeneticsRecombinationSelection

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Area of Science:

  • Virology
  • Genomics
  • Molecular Evolution

Background:

  • Recombination is a key driver of genetic diversity and evolution in coronaviruses.
  • Recombination patterns in coronaviruses are non-random, influenced by genomic sequence features and selective pressures.

Purpose of the Study:

  • To identify conserved recombination patterns across six coronavirus subgenera.
  • To determine the factors underlying conserved recombination patterns in coronaviruses.

Main Methods:

  • Analysis of whole-genome sequence data from six coronavirus subgenera.
  • Identification of conserved recombination hotspots and coldspots.
  • Correlation of recombination breakpoint locations with genomic features.

Main Results:

  • Recombination breakpoints in coronaviruses are non-random and conserved across subgenera.
  • Transcriptional regulatory sequences are major determinants of recombination hotspot locations.
  • Breakpoints favor low GC content, non-coding regions, gene edges, and minimally disruptive Spike gene sites.

Conclusions:

  • Genomic sequence features, particularly transcriptional regulatory sequences, significantly influence coronavirus recombination.
  • Selection against disruptive protein folding also shapes observed recombination patterns.
  • Understanding these patterns is crucial for comprehending coronavirus evolution and adaptation.