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Related Concept Videos

Viral Recombination00:57

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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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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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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.
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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Updated: Jan 10, 2026

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A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2.

Shing H Zhan1,2,3, Yan Wong1,4, Anastasia Ignatieva5,4

  • 1Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, United Kingdom.

Biorxiv : the Preprint Server for Biology
|November 26, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces sc2ts, a new method to analyze SARS-CoV-2 genome data by inferring complex genealogies called Ancestral Recombination Graphs (ARGs). This approach accurately captures the impact of recombination in viral evolution.

Keywords:
ARGAncestral recombination graphsSARS-CoV-2recombinationtskit

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Area of Science:

  • Genomics
  • Epidemiology
  • Computational Biology

Background:

  • The COVID-19 pandemic generated millions of SARS-CoV-2 genome sequences, creating a rich dataset for evolutionary analysis.
  • Traditional phylogenetic methods assume negligible recombination, representing viral genealogies as simple trees, which is insufficient given the prevalence of recombinant lineages.

Purpose of the Study:

  • To develop and apply a scalable method for inferring reticulate (non-tree-like) genealogies from large viral genomic datasets.
  • To accurately represent the evolutionary history of SARS-CoV-2, accounting for recombination events.

Main Methods:

  • Development of sc2ts, a novel method for real-time inference of Ancestral Recombination Graphs (ARGs) at pandemic scale.
  • Application of sc2ts to infer an ARG for 2.48 million SARS-CoV-2 genomes.
  • Leveraging the tskit software ecosystem for efficient data handling, analysis, and visualization.

Main Results:

  • Inference of a large-scale ARG for 2.48 million SARS-CoV-2 genomes, providing a detailed view of viral evolution.
  • Clarification of relationships among recombinant SARS-CoV-2 lineages.
  • Quantification of the rate of recombination over time and establishment of a lower bound for detectable recombination.

Conclusions:

  • The sc2ts method provides a powerful tool for understanding viral evolution in the presence of recombination.
  • The inferred ARG offers a validated resource for further downstream analyses and visualizations of SARS-CoV-2 evolution.
  • This work highlights the importance of considering recombination in phylogenetic studies of rapidly evolving viruses like SARS-CoV-2.