HIV-1 population characteristics in the CSF compartment.

aThe percent of CSF env sequences that were compartmentalized at each sampling time point. CSF env sequences were considered compartmentalized based on maximum-likelihood phylogenetic tree structures and strong bootstrap support. The 95% confidence intervals were calculated for the proportion of CSF-compartmentalized env sequences using the modified Wald method.bThe classification of clonal amplification was determined by calculating the average overall pairwise distance (nucleotide substitutions per site) between env sequences in the compartmentalized HIV-1 population. A CSF-compartmentalized HIV-1 population with an average pairwise distance cThe Slatkin-Maddison test for gene flow between populations was used to measure genetic compartmentalization between the blood plasma and CSF HIV-1 populations. Migration events describe the number of env migration events between the blood plasma and CSF HIV-1 populations for each phylogenetic tree. A P-value dHIV-1 population characteristics in the CSF compartment. Eq, equilibration with the blood plasma; Intermediate, a subpopulation of the CSF is compartmentalized; Comp, significant compartmentalization in the CSF; Amp, clonal amplification of variants detected in the CSF; N/A, not applicable.