. 2008 Feb 6;82(8):3952–3970. doi: 10.1128/JVI.02660-07

TABLE 3.

Diversity of SGA-direct sequence-derived complete env genes in subjects with primary HIV-1 infections

Subject	Fiebig stage	Date sample collected (mo/day/yr)	No. of SGA env amplicons	Nucleotide sequence length	Nucleotide sequence diversity		Amino acid sequence diversity		Time to MRCA^a (days)	Viral complexity	No. of variants transmitted
Subject	Fiebig stage	Date sample collected (mo/day/yr)	No. of SGA env amplicons	Nucleotide sequence length	Mean	Range	Mean	Range	Time to MRCA^a (days)	Viral complexity	No. of variants transmitted
ZM184F	V	07/10/03	26	2604-2621	0.13	0.00-0.31	0.33	0.00-0.80	43	Homogeneous	1
ZM214M	VI	07/02/03	35	2544-2568	0.45	0.00-1.10	0.93	0.00-2.00	231	Heterogeneous^b	>1
ZM215F	VI	10/19/02	32	2502-2580	4.26	0.00-7.38	7.32	0.00-13.4	1,869	Heterogeneous	≥4
ZM246F	II	01/14/03	27	2532	0.05	0.00-0.20	0.10	0.00-0.36	26	Homogeneous	1
	VI	04/04/03	14	2531-2532	0.31	0.16-0.40	0.58	0.24-0.95	107
ZM247F	II	10/28/03	25	2583-2595	1.12	0.00-2.74	1.78	0.00-4.40	788^c	Heterogeneous	2
	III	11/01/03	19	2592-2595	0.56	0.00-2.70	0.90	0.00-4.29	774
ZM249M	IV	08/05/03	24	2562-2563	0.07	0.00-0.27	0.16	0.00-0.82	31	Homogeneous	1
	V	08/12/03	25	2562	0.05	0.00-0.16	0.14	0.00-0.47	16
ZM178F	VI	01/18/03	26	2560-2613	0.41	0.00-0.67	0.99	0.00-1.85	112	Homogeneous	1
ZM180M	V	07/20/02	24	2588-2560	0.23	0.04-0.39	0.47	0.00-1.06	71	Homogeneous	1
ZM206F	VI	07/13/02	35	2538-2560	0.25	0.04-0.47	0.61	0.00-1.29	73	Homogeneous	1
ZM229M	VI	10/19/02	29	2526-2592	2.28	0.04-5.82	4.08	0.00-10.3	1,502	Heterogeneous	≥4
ZM231F	V	12/17/02	48	2513-2545	0.13	0.00-0.43	0.32	0.00-1.30	73	Homogeneous	1
ZM235F	V	12/20/02	28	2244-2565	0.16	0.00-0.39	0.34	0.00-0.82	54	Homogeneous	1

The time to the MRCA was estimated by using the average branch length to root of midpoint-rooted neighbor-joining trees (inferred after excluding gaps and with Kimura's two-parameter correction) assuming a rate of 1.7 × 10⁻⁵ substitutions per site per day (estimated from the extent of env sequence divergence in subject ZM246F).

The number of transmitted variants could not be determined.

The time to the MRCA for sequences within each of the two discrete transmitted virus lineages in subject ZM247F was estimated to be between 10 and 31 days.