Subject population virologic, clinical and phylogenetic characteristics.

aTime point(s) beyond 2 years p.i. analyzed for subject 9018 and 9040 were not included in any overall population analyses.bEstimated.c,dVL, viral load; HIV-1 RNA (log10 copies/ml).eCells/μl.fCSF white blood cell (WBC) count, cell/μl.gCSF/plasma albumin ratio.hThree statistical analyses of genetic compartmentalization between viral populations in the blood plasma and CSF: Slatkin-Maddison test (SM) [18], Wright’s measure of population subdivision (Fst) [19,20] and the Nearest-neighbor statistic (Snn) [21]. P values iHIV-1 population characteristics in the CSF compartment (compart). Eq, equilibrated blood plasma and CSF populations; Cp (compartmentalized), significant compartmentalization by three compartmentalization analyses; Ap, clonal amplification of ≥3 variants detected in the CSF.[18]jTMRCA (Time to Most Recent Common Ancestor) of the entire viral population, analyzed by BEAST [15]. An asterisk (*) indicates transmission of > 1 variant.kTMRCA for the compartmentalized (Comp) CSF population for compartmentalized subjects.lPatient 9018 diagnosed with neurosyphilis at indicated date.mSignificant compartmentalization scores were due to a compartmentalized lineage in the plasma. After removing this plasma lineage, the remaining plasma and CSF sequences were equilibrated.Subject population virologic, clinical and phylogenetic characteristics.