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Codon volatility does not reflect selective pressure on the HIV-1 genome
Satish K Pillai1, Sergei L Kosakovsky Pond, Christopher H Woelk
1University of California, San Diego, Stein Clinical Research Building, Room 325, 9500 Gilman Drive 0679, La Jolla 92093, USA.
Virology
|May 17, 2005
Summary
Codon volatility, a measure of how mutations change amino acids, was tested as an indicator of selection pressure in HIV-1. This study found codon volatility is not a reliable indicator of selection pressure.
Area of Science:
- Molecular Biology
- Evolutionary Biology
- Virology
Background:
- Codon volatility quantifies the impact of point mutations on amino acid sequences.
- Previous research suggested cumulative gene volatility indicates genome-wide selection pressure.
Purpose of the Study:
- To evaluate codon volatility as a measure of selection pressure in HIV-1 subtype B.
- To compare codon volatility estimates with established phylogenetic methods.
Main Methods:
- Calculated codon volatility for all available full-length HIV-1 subtype B genomes.
- Compared volatility estimates with results from likelihood- and distance-based comparative methods.
Main Results:
- Codon volatility did not correlate with established methods for assessing selection pressure.
- The study found no significant relationship between codon volatility and selection indicators.
Conclusions:
- Codon volatility is not a reliable indicator of selection pressure in HIV-1.
- Established comparative methods remain the standard for selection pressure analysis in viral genomes.