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Related Experiment Video

Updated: Jan 3, 2026

In Vitro Disassembly of Influenza A Virus Capsids by Gradient Centrifugation

In Vitro Disassembly of Influenza A Virus Capsids by Gradient Centrifugation

Published on: March 27, 2016

Dinucleotide evolutionary dynamics in influenza A virus.

Haogao Gu¹, Rebecca L Y Fan¹, Di Wang²

¹School of Public Health, LKS Faculty of Medicine, G/F, Patrick Manson Building (North Wing), 7 Sassoon Road, Pokfulam, Hong Kong.

Virus Evolution

|November 19, 2019

Summary

Influenza A virus shows biases in dinucleotide composition, with CpG and UpA under-represented. Temporal analysis reveals decreased CpG frequency in seasonal H1 virus, impacting evolution and codon usage.

Keywords:

codon usage dinucleotide usage evolution influenza

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Area of Science:

Virology
Genomics
Evolutionary Biology

Background:

RNA viruses, including influenza A virus, exhibit significant dinucleotide composition biases.
Altered CpG usage in influenza mutants leads to attenuation in mammalian models, but the link to codon usage bias and evolutionary changes remains unclear.

Purpose of the Study:

Investigate dinucleotide usage patterns across influenza virus segments and groups.
Analyze temporal changes in dinucleotide frequency and their relationship with codon usage bias and evolutionary pressures.

Main Methods:

Applied a Monte Carlo method to identify under-represented/over-represented dinucleotide motifs in influenza viral sequences.
Accounted for biases from codon usage and amino acid sequences.
Analyzed temporal variations in dinucleotide frequency, particularly in seasonal H1 virus post-1977.

Main Results:

CpG and UpA dinucleotides are under-represented, while UpG and CpA are over-represented across all viral segments.
A significant decrease in CpG frequency was observed in specific segments of the seasonal H1 virus after 1977.
Silent mutations primarily drive these temporal dinucleotide variations, leading to altered codon usage bias.

Conclusions:

Dinucleotide preference directly influences synonymous codon usage bias in influenza viruses.
Understanding these dinucleotide dynamics provides insights into the evolutionary history and selection pressures shaping the influenza virus genome.