Subject population virological and phylogenetic characteristics.

a,bVL, viral load; HIV-1 RNA (log10 copies/ml).
cCSF/blood VL ratio.
dThe percent of CSF env sequences that were compartmentalized (comp.) for each subject. CSF env sequences were considered compartmentalized when ≥4 sequences were found within the same clade and bootstrap values ≥40 were observed.
eP values used to measure genetic compartmentalization between the blood plasma and CSF HIV-1 populations were obtained using the Slatkin-Maddison test for gene flow between populations [31]. A P value<0.05 indicated statistically significant genetic compartmentalization.
fP value<0.05 was obtained for subject 3040, but visual assessment of the neighbor-joining tree structure indicated the presence of an additional HIV-1 population within the blood plasma that was largely absent from the CSF.
gP value<0.05 was obtained for subject 4013, but visual assessment of neighbor-joining tree structure indicated significant compartmentalization was not present.
hHIV-1 population characteristics in the CSF compartment (compart). Eq, equilibrated blood plasma and CSF populations; Inter (Intermediate), a minor subpopulation of the CSF was compartmentalized; Comp, significant compartmentalization in the CSF; Amp, clonal amplification of ≥3 variants detected in the CSF; N/A, not applicable when the CSF viral load was too low to obtain enough CSF env sequences.
iThe time to most recent common ancestor (TMRCA) analyzed by Bayesian Evolutionary Analysis by Sampling Trees (BEAST) [33].
jFor patient 4004, ≥3 transmitted variants observed: the first variant evolved at 52 months; the second and third variants evolved at 47 months.
kNumber of variants transmitted.
lTMRCA for compartmentalized (Comp) population for intermediate and compartmentalized subjects. Equilibrated subjects were not analyzed (N/A). When recombination occurred between transmitted variants, BEAST was unable to date TMRCA (*).