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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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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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Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
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Horizontal gene transfer (HGT) is a process where genetic material moves between organisms within the same generation, unlike vertical gene transfer, which occurs from parent to offspring. HGT plays a crucial role in microbial evolution, adaptation, and survival, particularly in shared environments like the human gut.Mobile genetic elements such as plasmids, prophages, integrons, insertion sequences, and transposons facilitate this process. HGT occurs through three primary mechanisms:...
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Viral Mutations00:36

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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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Related Experiment Video

Updated: Sep 4, 2025

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Published on: May 26, 2013

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ViQUF: De Novo Viral Quasispecies Reconstruction Using Unitig-Based Flow Networks.

Borja Freire, Susana Ladra, Jose R Parama

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |July 19, 2022
    PubMed
    Summary
    This summary is machine-generated.

    ViQUF is a new tool for viral quasispecies assembly that reconstructs viral haplotypes from sequencing data. It is faster and uses less memory than previous methods while maintaining high accuracy.

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    Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
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    Area of Science:

    • Virology
    • Bioinformatics
    • Computational Biology

    Background:

    • Viral infections lead to diverse viral populations (quasispecies) through mutation and recombination.
    • Reconstructing these viral haplotypes from sequencing data is crucial for understanding viral evolution and disease.
    • Existing methods for de novo viral quasispecies assembly face challenges in speed and memory efficiency.

    Purpose of the Study:

    • To develop an efficient and accurate de novo assembler for viral quasispecies.
    • To address both haplotype assembly and frequency quantification.
    • To improve upon existing computational methods for viral population reconstruction.

    Main Methods:

    • ViQUF utilizes a de Bruijn graph for initial assembly.
    • It employs a min-cost flow algorithm on a paired-end information-based flow network to create an approximate paired assembly graph with frequency estimations.
    • Greedy path reconstruction guided by the min-cost flow solution is used to identify original haplotypes.

    Main Results:

    • ViQUF demonstrates significant speed improvements, being at least four times faster than previous methods.
    • It uses substantially less memory, requiring at most half the memory of comparable tools.
    • The assembler maintains high quality in both haplotype assembly and frequency estimation, comparable to or better than slower overlap graph-based methods.

    Conclusions:

    • ViQUF offers a computationally efficient solution for de novo viral quasispecies assembly.
    • The tool effectively reconstructs and quantifies viral haplotypes, advancing the study of viral evolution.
    • ViQUF provides a valuable alternative for researchers needing fast and accurate viral population analysis from sequencing data.