Adaptation to different human populations by HIV-1 revealed by codon-based analyses

Area of Science:

• Evolutionary biology
• Genomics
• Virology

Background:

• Detecting adaptive evolution in protein-coding sequences often uses codon-based methods.
• Existing methods do not identify specific sites under differential selection between populations.
• Population comparisons are crucial for understanding natural selection.

Purpose of the Study:

• To develop novel methods for identifying codon sites under differential selection in two populations.
• To analyze adaptive evolution in human immunodeficiency virus (HIV) populations.
• To pinpoint specific amino acid sites with population-specific selection pressures.

Main Methods:

• Development of two fixed effects maximum likelihood (FEMS) methods.
• Method 1: Identifies codon positions with persistent selection patterns within a population.
• Method 2: Detects differential selection on individual codons between two sampled populations.

Main Results:

• Few positively selected amino acid sites in HIV persist long-term within populations.
• Many detected changes occur at the tips of phylogenetic trees and may be deleterious.
• Seven amino acid sites in HIV protease and reverse transcriptase show differential selection between the two populations studied.

Conclusions:

• The new FEMS methods effectively identify population-specific adaptive evolution.
• HIV exhibits specific adaptations to distinct human host populations, particularly at seven identified amino acid sites.
• Understanding differential selection is key to comprehending pathogen adaptation and evolution.