. 2009 Jun 17;83(17):8470–8481. doi: 10.1128/JVI.02568-08

TABLE 1.

Analysis of population structure between provirus derived from activated and resting CD4⁺ T cells

Patient^a	Gene amplified	PPC present^b	No. of independent sequences in cells		SM analysis^c				AMOVA analysis					Molecular diversity (π)
			Activated cells	Resting cells	P		Adjusted P^d		Migration events (ML/BI)	% Variation among or within populations		P	Adjusted P	Activated CD4⁺ T cells	Resting CD4⁺ T cells
			Activated cells	Resting cells	ML	BI	ML	BI	Migration events (ML/BI)	% Variation among or within populations		P	Adjusted P	Activated CD4⁺ T cells	Resting CD4⁺ T cells
154*	RT	Yes	24	242	0.130	0.140	0.170	0.209	22/22	-0.25	100.25	0.602	0.63	0.019	0.020
1†	Env	NA	28	32	0.103	0.537	0.170	0.604	17/20	1.19	98.81	0.117	0.263	0.028	0.018
2†	Env	NA	23	20	0.683	0.504	0.768	0.604	15/14	1.07	98.93	0.240	0.309	0.117	0.096
4†	Env	NA	21	22	0.106	0.043	0.170	0.097	12/11	0.65	99.35	0.186	0.297	0.090	0.107
5†	Env	NA	21	17	0.022	0.036	0.100	0.095	9/9	10.75	89.25	0.025	0.075	0.065	0.035
7†	Env	NA	20	22	0.132	0.021	0.170	0.100	12/10	1.97	98.03	0.198	0.297	0.066	0.054
8†	Env	NA	21	17	0.871	0.871	0.871	0.871	14/14	-0.94	100.94	0.633	0.633	0.034	0.038
J2‡	Env	NA	22	20	0.002	0.000	0.018	0.000	8/8	19.73	80.27	0.000	0.000	0.080	0.095
J7‡	Env	NA	28	28	0.120	0.112	0.170	0.112	16/16	4.02	95.98	0.022	0.075	0.067	0.091

*, Patient sequences derived from Bailey et al. (1); †, patient sequences derived from Chun et al. (10); ‡, patient sequences derived from Chun et al. (11).

A PPC was previously defined as being a sequence that represented >50% of all independent sequences from the plasma and <1% of all independent proviral sequences from the resting CD4⁺ T-cell compartment (1). NA, not applicable (patients could not be evaluated for the presence of a PPC).

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

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