TABLE 1.

Genetic diversity in subjects' samples early in infection

Subject	PNSa	Risk factor(s)b	No. of samples sequenced	Nucleotide distancec	Amino acid difference (%)d	Insertions/deletionse
U.S. women
F14	91	IDU, HSC	7	0.86-3.25	2.00-7.49	18 bp in V4
F2	148	IDU	4	0.77-2.71	2.02-5.02	30 bp in V1
F15	49	IDU	6	0.67-2.34	1.15-4.60	3 bp in V2 and V5
F7	247	HSC	4	0.59-1.68	1.17-3.81	39 bp in C3
F3	191	HSC	4	0.54-1.54	1.18-3.81	39 bp in V1
F9	234	IDU	5	0.62-1.08	1.17-2.62	66 bp in C2
F5	114	IDU, HSC	4	0.57-1.03	0.86-2.22	27 bp in V1
F10	118	HSC	4	0.56-1.09	0.83-2.71	24 bp in V1
F16	99	IDU, HSC	5	0.09-0.54	0.00-1.08	3 bp in V2
F4	126	IDU, HSC	2	0.49	1.16	16 bp in C2
F11	165	HSC	NAf	NA	NA	NA
MEM	6	HSC	NA	NA	NA	NA
K-C	10	HSC	NA	NA	NA	NA
U.S. men
M3	249	IDU	4	2.33-4.32	4.50-7.60	21 bp in V1
M1	142	MSM	7	0.38-1.52	0.56-3.67	21 bp in V1
M4	250	IDU	3	0.41-0.92	0.61-2.45	50 bp in C4
M2	188	MSM	NA	NA	NA	NA
Kenyan men
T135	230	HSC	5	0.51-3.20	1.51-6.67	15 bp in V2
T263	283	HSC	2	0.97	2.31	15 bp in V4
T199	322	HSC	3	0.38-0.88	0.86-2.35	15 bp in V4
T158	139	HSC	NA	NA	NA	NA
T387	280	HSC	NA	NA	NA	NA
T457	28	HSC	NA	NA	NA	NA
T518	280	HSC	NA	NA	NA	NA
T594	133	HSC	NA	NA	NA	NA
T645	273	HSC	NA	NA	NA	NA
T650	161	HSC	NA	NA	NA	NA

^aPNS (post-negative serology), number of days between the last negative HIV-1 serology test and the time of sample collection.

^bSuspected route of HIV-1 acquisition. IDU, injection drug use; HSC, heterosexual contact; MSM, men having sex with men.

^cRange of Kimura two-parameter pairwise substitution rates per 100 bases, ignoring insertions and deletions

^dRange of pairwise percentage differences, ignoring insertions and deletions.

^eLargest insertion or deletion between sequence pairs and the envelope region.

^fNA, not applicable because no heteroduplexes were detected by HMA and therefore sequence analysis was not performed.