TABLE 4.

Analysis of population structure between free plasma virus and provirus after removal of all PPCs

Patient or patient 154 extended-analysis typea	Gene amplified	No. of independent sequences		SM analysisb					AMOVA analysis				Molecular diversity (π)
		Free plasma virus	Integrated provirus	P		Adjusted Pc		Migration events (ML/BI)	% Variation among or within populations		P	Adjusted P	Free plasma virus	Provirus
				ML	BI	ML	BI
Patient
113*	RT	14	24	0.432	0.219	0.432	0.229	11/10	-1.45	101.45	0.704	0.704	0.009	0.013
135*	RT	31	151	0.000	0.000	0.000	0.000	16/18	2.34	97.66	0.037	0.046	0.025	0.024
139*	RT	15	83	0.000	0.000	0.000	0.000	16/16	17.59	82.41	0.000	0.000	0.029	0.021
148*	RT	9	138	0.006	0.008	0.008	0.011	11/11	11.01	88.99	0.005	0.008	0.021	0.020
154*	RT	75	242	0.000	0.000	0.000	0.000	42/44	6.68	93.32	0.000	0.000	0.021	0.020
154*	Env	46	28	0.004	0.003	0.007	0.005	16/16	4.60	95.40	0.018	0.026	0.063	0.068
209†	Env	179	113	0.000	0.000	0.000	0.000	17/16	1.66	98.34	0.055	0.061	0.067	0.077
Patient 154 extended analysis
Plasma virus vs provirus derived from activated CD4+ T Cells	Env	75	25	0.035	0.229	0.039	0.229	19/21	5.57	94.43	0.001	0.002	0.021	0.019
Plasma virus vs provirus derived from monocytes	Env	75	17	0.005	0.020	0.007	0.025	12/13	8.13	91.87	0.001	0.002	0.021	0.020
Plasma virus vs provirus derived from unfractionated PBMC	Env	75	83	0.000	0.000	0.000	0.000	35/36	6.11	93.89	0.000	0.000	0.021	0.021

^a*, Patient sequences derived from Bailey et al. (1); †, new patient analyzed for this study.

^bML, phylogenetic trees were generated via a classical ML approach; BI, phylogenetic trees were generated via a Bayesian inference approach.

^c“Adjusted P” refers to P values obtained for both the SM tests and the AMOVA tests were subjected to Benjamini-Hochberg FDR corrections, treating P values obtained using the ML approach separately from those obtained using BI and both separately from the AMOVA tests (2).