Table 2.

Compartmentalization Analysis for partial env HIV RNA in blood and seminal plasma and HIV DNA in PBMC

Subject	Days from EDI	Location		Fst test*	P value	Compartmentalization
S1	20	BP	PBMC	0.01	0.09	NO
		PBMC	SP	0.05	0.06#	NO
		BP	SP	−0.09	1.00	NO
	104	PBMC	SP	0.00	0.16	NO
		BP	SP	0.92	0.01	YES
		BP	PBMC	0.92	0.01#§	NO
S2	87	BP	SP	−0.03	0.01	NO
	289	BP	SP	0.26	0.01	YES
S3	98	PBMC	SP	0.49	0.01	YES
		BP	SP	0.52	0.01	YES
		BP	PBMC	0.00	0.01	NO
	182	BP	SP	−0.06	0.85	NO
S4	40	BP	SP	−0.15	1.00	NO
		BP	PBMC	−0.37	1.00	NO
		PBMC	SP	0.13	0.01#§	NO
	47	BP	SP	0.96	0.01	YES
	75	BP	SP	0.34	0.01	YES
	118	BP	PBMC	0.21	0.01#§	NO
S5	77	BP	SP	−0.05	0.03	NO
		BP	PBMC	−0.37	1.00	NO
		PBMC	SP	−0.24	1.00	NO
	162	BP	SP	0.97	0.01	YES
	254	BP	SP	0.17	0.01	YES
S6	177	BP	SP	0.10	0.01	YES
		BP	PBMC	−0.01	0.01	NO
		PBMC	SP	0.06	0.01	YES
	457	BP	SP	−0.17	0.96	NO

Compartmentalization is called when all tests indicate compartmentalization [see text]

^#Indicates tests which become significant (or not significant) if copy numbers are ignored during F_ST calculations.

^§Indicates tests, which become insignificant under the phylogeny-based Slatkin-Maddison test [see text]. Statistical significance was derived via a 1,000-fold population-structure randomization/permutation test.

BP: Blood Plasma, SP: Seminal Plasma; PBMC: Peripheral Blood Mononuclear Cells; EDI: estimated date of infection.

^*While, F_ST could assume negative values, none of the samples with negative F_ST could be called compartmentalized.