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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...

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.

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Related Experiment Video

Updated: Sep 8, 2025

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

Algorithms for Short-Read Viral Haplotype Reconstruction: Challenges, Solutions, and Perspectives.

Wing-Yan Joyce Sung¹, Jasmijn A Baaijens²

¹Delft University of Technology, Delft, The Netherlands.

Methods in Molecular Biology (Clifton, N.J.)

|July 30, 2025

Summary

This summary is machine-generated.

Reconstructing viral haplotypes from next-generation sequencing data is complex due to genetic diversity and short reads. This review explores strategies to improve the accuracy and efficiency of viral genetic diversity analysis for better public health insights.

Keywords:

Abundance estimation Haplotype assembly Minor variants Viral quasispecies Within-host diversity

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Last Updated: Sep 8, 2025

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

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

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:

RNA viruses like HIV, HCV, and SARS-CoV-2 exhibit significant intrahost genetic diversity.
Multiple viral haplotypes can coexist within a single host infection.
Next-generation sequencing (NGS) enables the study of this diversity.

Purpose of the Study:

To review current computational strategies for reconstructing full-length viral haplotypes from NGS data.
To identify challenges in viral haplotype reconstruction, including low-frequency mutants, sequencing errors, and read length limitations.
To highlight future directions for enhancing the accuracy and efficiency of viral haplotype reconstruction.

Main Methods:

Review of existing computational methods and algorithms for viral haplotype reconstruction.
Analysis of challenges posed by high sequencing depth, short reads, and genetic variation.
Discussion of strategies to overcome computational hurdles in analyzing viral genetic diversity.

Main Results:

Full-length haplotype reconstruction from short NGS reads is computationally intensive.
Low-frequency mutants, sequencing errors, and insufficient read length complicate accurate reconstruction.
Development of efficient algorithms is crucial for handling large datasets generated by deep sequencing.

Conclusions:

Accurate and efficient viral haplotype reconstruction is essential for understanding viral evolution.
Improved methods will aid in developing more effective treatment strategies against viral infections.
Advances in this field will significantly inform public health interventions and disease control efforts.