Analyses
Viral load and CD4+ counts Viral load and CD4+ counts Genome sequences Genome sequences Consensus sequences Consensus sequences Phylogenetic trees Phylogenetic trees Divergence and diversity Divergence and diversity Local divergence and diversity Local divergence and diversity Coverage Coverage Single nucleotide polymorphisms Single nucleotide polymorphisms Haplotypes Haplotypes

Single nucleotide polymorphisms

Mutations at different sites are present at different frequencies in the viral population. These frequencies change in time. Frequency changes are caused by depending on interactions with the host immune system and other selective pressures, by linkage and hitchhiking (genetic draft), and by genetic drift.