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Size and Structure of Viral Genomes

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...

Evolution of Microbial Genome

Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.

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 for adaptive...

Retrovirus Life Cycles

Retrovirus Life Cycles

Retroviruses have a single-stranded RNA genome that undergoes a special form of replication. Once the retrovirus has entered the host cell, an enzyme called reverse transcriptase synthesizes double-stranded DNA from the retroviral RNA genome. This DNA copy of the genome is then integrated into the host’s genome inside the nucleus via an enzyme called integrase. Consequently, the retroviral genome is transcribed into RNA whenever the host’s genome is transcribed, allowing the retrovirus to...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Gene Duplication and Divergence

Gene Duplication and Divergence

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.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

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Related Experiment Video

Updated: May 17, 2026

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

Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data.

Art F Y Poon¹, Luke C Swenson, Evelien M Bunnik

¹BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada. apoon@cfenet.ubc.ca

Plos Computational Biology

|November 8, 2012

Summary

This summary is machine-generated.

Human immunodeficiency virus (HIV) evolution towards CXCR4 coreceptor use is patient-specific, with mutations appearing months before detectable changes. This suggests the

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Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

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Amplifying and Quantifying HIV-1 RNA in HIV Infected Individuals with Viral Loads Below the Limit of Detection by Standard Clinical Assays

Amplifying and Quantifying HIV-1 RNA in HIV Infected Individuals with Viral Loads Below the Limit of Detection by Standard Clinical Assays

Published on: September 26, 2011

Area of Science:

Virology
Evolutionary Biology
Immunology

Background:

Human immunodeficiency virus (HIV)-1 initially uses CCR5 for entry.
Switch to CXCR4 coreceptor use accelerates CD4+ T-cell decline and AIDS progression.
A 'fitness valley' is hypothesized to influence the CCR5 to CXCR4 switch.

Purpose of the Study:

To investigate the evolutionary dynamics of HIV coreceptor switching within hosts.
To discriminate between competing models of HIV coreceptor switch.
To determine the timing and pathways of mutations leading to CXCR4 usage.

Main Methods:

Phylogenetic pipeline for molecular clock analysis and ancestral reconstruction.
Next-generation sequencing of HIV RNA from longitudinal samples.
Prediction of HIV coreceptor usage from ancestral sequences using geno2pheno.

Main Results:

Mutations for CXCR4 use emerged ~16 months before predicted CXCR4-using ancestors.
Cell-based CXCR4 assay positivity followed predicted usage by ~10 months.
CXCR4 usage arose in multiple lineages in 5/8 subjects; extinct lineages were common.
Mutation accumulation varied significantly between patients, indicating genotype-dependent fitness valley effects.

Conclusions:

HIV coreceptor switch dynamics are highly patient-specific.
The role of a fitness valley in coreceptor switching is contingent on the transmitted HIV genotype.
Phylogenetic analysis provides insights into the evolutionary timing of critical viral mutations.