TABLE 3.

Genetic distances for linked Zambian transmission pairs

Sample ID	Sample collection date (mo-day-yr)	Subgenomic regiona	Cutoff valueb	Pairwise distancec	Subtype
47	6-5-98	gagA (242)	2.5	0.0	C
67	6-8-98	gagA	2.5	0.4	C
82	10-19-98	gagA	2.5	1.7	C
89	6-13-98	gagA	2.5	0.4	C
114	8-2-98	gagA	2.5	0.8	C
119	8-9-98	gagA	2.5	0.0	C
4	11-15-98	gagB (285)	4.3	1.1	C
11	6-6-98	gagB	4.3	1.1	C
23	8-7-98	gagB	4.3	0.4	C
16	2-10-98	gagB	4.3	0.7	C
17	8-9-96	gagB	4.3	0.0	C
25	6-12-97	gagB	4.3	2.5	C
29	6-7-98	gagB	4.3	4.0	C
33	6-8-98	gagB	4.3	0.7	C
42	7-22-96 (F)	gagB	4.3	0.0	C
8-9-96 (M)
49	7-9-96	gagB	4.3	0.4	C
1	10-16-98	gagC (317)	4.5	2.3	C
2	7-4-98	gagC	4.5	2.0	C
5	6-15-98	gagC	4.5	0.6	C
10	2-14-96	gagC	4.5	1.3	C
30	6-8-98	gagC	4.5	0.0	C
71	9-5-98	gagC	4.5	1.7	C
20	10-15-98	gagD (406)	3.1	1.5	A
56	6-6-98	gagD	3.1	1.5	A
142	8-13-98	gagD	3.1	1.0	A
46	6-7-98	gagD	4.6	0.5	C
55	8-13-98	gagD	4.6	0.8	C
62	6-6-98	gagD	4.6	2.2	C
103	7-8-98	gagD	4.6	1.1	C
76	6-25-98	gagE (458)	3.5	0.9	C
101	6-20-98	gagE	3.5	0.4	C
108	6-19-98 (F)	gagE	3.5	1.1	C
6-20-98 (M)
124	8-15-98	gagE	3.5	0.2	C
37	6-8-98	gagF (381)	3.2	2.1	C
51	6-6-98	gagF	3.2	2.4	C
58	6-19-98	gagF	3.2	0.3	C
64	8-6-98	gagF	3.2	1.1	C
70	8-27-98	gagF	3.2	1.1	C
68	8-9-98	gagG (445)	3.6	2.5	C
92	6-8-98	gagG	3.6	0.9	C
97	6-6-98	gagG	3.6	2.9	C
99	6-6-98	gagG	3.6	0.2	C
102	6-23-98	gagG	3.6	1.4	C
105	7-21-98	gagG	3.6	1.4	C
106	6-8-98	gagG	3.6	1.1	C
110	8-20-98	gagG	3.6	0.5	C
22	6-7-98	gagH (373)	3.7	3.1	C
73	6-6-98	gagH	3.7	0.8	C
21	8-21-98 (F)	gp120A (373)	5.0	2.5	C
5-31-98 (M)
60	6-6-98	gp120A	5.0	0.6	C
113	8-7-98	gp120A	5.0	1.9	C
131	8-23-98	gp120A	5.0	0.0	C
66	11-6-98	gp120B (296)	3.2	0.3	C
75	8-7-98	gp120B	3.2	1.7	C
78	6-30-98	gp120B	3.2	0.3	C
83	8-10-98	gp120B	3.2	1.0	C
90	6-6-98	gp120B	3.2	0.7	C
122	11-12-98	gp120B	3.2	1.0	C
136d	10-13-99	gp41 (411)	2.6	2.7e	D
43	3-16-97 (F)	gp41	3.8	1.0	G
6-24-98 (M)
91	6-6-98	gp41	3.8	2.3	G
148	3-4-00	gp41	3.8	0.5	G
98d	8-19-97 (F)	gp41	n/a	3.8	J
10-26-98 (M)
3	9-9-99	gp41	5.4	0.5	C
6	2-16-00	gp41	5.4	1.5	C
8	7-29-96	gp41	5.4	2.5	C
12	6-6-00	gp41 (411)	5.4	1.8	C
13	9-12-99	gp41	5.4	0.8	C
14	10-28-99	gp41	5.4	0.6	C
15	9-23-99	gp41	5.4	1.8	C
19	6-6-98	gp41	5.4	2.3	C
24	7-13-96	gp41	5.4	1.8	C
26	11-4-99	gp41	5.4	0.0	C
27	4-15-97	gp41	5.4	1.1	C
28	5-16-96	gp41	5.4	0.5	C
32	8-6-99	gp41	5.4	0.8	C
34	6-14-96 (F)	gp41	5.4	1.5	C
5-14-96 (M)
35	12-12-97 (F)	gp41	5.4	2.0	C
10-12-96 (M)
36	8-25-99	gp41	5.4	0.3	C
38	4-8-00	gp41	5.4	1.8	C
39	8-27-99	gp41	5.4	1.1	C
40	7-25-97 (F)	gp41	5.4	2.5	C
10-16-98 (M)
41	10-20-99	gp41	5.4	2.8	C
45	3-29-00	gp41	5.4	2.2	C
48	9-3-99 (F)	gp41	5.4	1.5	C
9-19-00 (M)
50	9-5-96	gp41	5.4	1.5	C
53	2-12-00	gp41	5.4	0.8	C
59	9-2-96	gp41	5.4	0.6	C
61	9-28-98	gp41	5.4	2.4	C
63	4-13-00	gp41	5.4	1.8	C
65	11-7-99	gp41	5.4	4.8	C
74	8-8-98	gp41	5.4	1.7	C
77	4-30-97	gp41	5.4	0.5	C
79	9-3-99 (F)	gp41	5.4	1.3	C
6-30-98 (M)
80	1-14-00	gp41	5.4	1.3	C
81	2-11-98	gp41	5.4	1.5	C
84	11-7-99	gp41	5.4	1.8	C
85	10-8-97 (F)	gp41	5.4	2.7	C
5-29-97 (M)
86	11-12-98	gp41	5.4	0.8	C
93	10-18-99	gp41	5.4	0.5	C
95	9-12-00	gp41	5.4	2.0	C
100	6-30-00	gp41	5.4	0.5	C
107	8-11-00 (F)	gp41	5.4	1.5	C
8-16-00 (M)
109	3-16-00	gp41	5.4	2.2	C
111	9-15-00	gp41	5.4	2.0	C
112	7-5-00	gp41	5.4	0.5	C
115	1-13-00	gp41	5.4	0.8	C
116	6-7-98	gp41	5.4	0.3	C
117	10-2-97	gp41	5.4	2.6	C
118	10-31-99	gp41	5.4	1.8	C
120	11-5-99	gp41	5.4	1.0	C
125	4-14-00	gp41	5.4	0.8	C
127	10-31-99	gp41	5.4	1.8	C
128	9-25-98	gp41	5.4	2.2	C
129	8-13-99	gp41	5.4	2.3	C
130	6-16-00 (F)	gp41	5.4	1.0	C
9-14-00 (M)
132	8-11-00	gp41	5.4	3.5	C
134	1-12-00	gp41	5.4	3.8	C
135	6-28-98	gp41	5.4	2.5	C
137	10-10-99	gp41	5.4	2.5	C
138	10-2-98	gp41	5.4	3.3	C
139	8-2-00	gp41	5.4	1.3	C
140	11-11-99	gp41	5.4	1.3	C
141	8-13-99	gp41	5.4	1.5	C
143	8-26-99	gp41	5.4	0.8	C
145	8-18-99	gp41	5.4	0.8	C
146	8-23-00	gp41	5.4	0.8	C
147	10-23-99	gp41	5.4	0.5	C
149	9-30-00	gp41	5.4	3.8	C

^aThe subgenomic region was analyzed as shown in Fig. 1. The subgenomic region size (in base pairs) is given in parentheses. F, female partner; M, male partner.

^bThe cutoff value is 2 SD below the mean (see Table 2).

^cPairwise distances are the percent sequence differences in the analyzed genomic region.

^dDetermined as epidemiologically linked by phylogenetic tree analysis.

^eGenetic distance is primarily due to G-to-A hypermutation.