Table S1: Sequences used for analyses
Sequence	Full Sequence Name	Accession number	Cohort^a	Date of Isolation (yr)	Country	Reference
A1Q23 17	A1.KE.94.Q23_17	AF004885		1994	Kenya	Neilson et al., 1999, (19)
A294CY017	A2.CY.94.94CY017_41	AF286237		1994	Cyprus	Gao et al., 2001, (8)
BHXB2	B.FR.83.HXB2	K03455		1983	France	Ratner et al., 1985, (26)
DELI	D.CD.83.ELI	K03454		1983	Dem. Rep. of Congo	Alizon et al., 1986, (1)
F193BR020	F1.BR.93.93BR020_1	AF005494		1993	Brazil	Gao et al., 1998, (7)
F2MP257	F2.CM.95.MP257	AJ249237		1995	Cameroon	Triques et al., 2000, (32)
GDRCBL	G.BE.96.DRCBL	AF084936		1996	Belgium	Oelrichs et al., 1999, (22)
HVI991	H.BE.93.VI991	AF190127		1993	Belgium	Janssens et al., 2000, (13)
JSE7022	J.SE.94.SE7022	AF082395		1994	Sweden	Laukkanen et al., 1999, (15)
KEQTB11C	K.CD.97.EQTB11C	AJ249235		1997	Dem. Rep. of Congo	Triques et al., 2000, (32)
00BW07621	C.BW.00.00BW07621	AF443088		2000	Botswana	Novitsky et al., 2002, (20)
00BW076820	C.BW.00.00BW076820	AF443089		2000	Botswana	Novitsky et al., 2002, (20)
00BW087421	C.BW.00.00BW087421	AF443090		2000	Botswana	Novitsky et al., 2002, (20)
00BW147127	C.BW.00.00BW147127	AF443091		2000	Botswana	Novitsky et al., 2002, (20)
00BW16162	C.BW.00.00BW16162	AF443092		2000	Botswana	Novitsky et al., 2002, (20)
00BW1686	C.BW.00.00BW1686	AF443093		2000	Botswana	Novitsky et al., 2002, (20)
00BW17593	C.BW.00.00BW17593	AF443094		2000	Botswana	Novitsky et al., 2002, (20)
00BW17732	C.BW.00.00BW17732	AF443095		2000	Botswana	Novitsky et al., 2002, (20)
00BW17835	C.BW.00.00BW17835	AF443096		2000	Botswana	Novitsky et al., 2002, (20)
00BW17956	C.BW.00.00BW17956	AF443097		2000	Botswana	Novitsky et al., 2002, (20)
00BW18113	C.BW.00.00BW18113	AF443098		2000	Botswana	Novitsky et al., 2002, (20)
00BW18595	C.BW.00.00BW18595	AF443099		2000	Botswana	Novitsky et al., 2002, (20)
00BW18802	C.BW.00.00BW18802	AF443100		2000	Botswana	Novitsky et al., 2002, (20)
00BW192113	C.BW.00.00BW192113	AF443101		2000	Botswana	Novitsky et al., 2002, (20)
00BW20361	C.BW.00.00BW20361	AF443102		2000	Botswana	Novitsky et al., 2002, (20)
00BW20636	C.BW.00.00BW20636	AF443103		2000	Botswana	Novitsky et al., 2002, (20)
00BW20872	C.BW.00.00BW20872	AF443104		2000	Botswana	Novitsky et al., 2002, (20)
00BW212721	C.BW.00.00BW2127214	AF443105		2000	Botswana	Novitsky et al., 2002, (20)
00BW21283	C.BW.00.00BW21283	AF443106		2000	Botswana	Novitsky et al., 2002, (20)
00BW22767	C.BW.00.00BW22767	AF443107		2000	Botswana	Novitsky et al., 2002, (20)
00BW38193	C.BW.00.00BW38193	AF443108		2000	Botswana	Novitsky et al., 2002, (20)
00BW38428	C.BW.00.00BW38428	AF443109		2000	Botswana	Novitsky et al., 2002, (20)
00BW38713	C.BW.00.00BW38713	AF443110		2000	Botswana	Novitsky et al., 2002, (20)
00BW3876 9	C.BW.00.00BW3876_9	AF443111		2000	Botswana	Novitsky et al., 2002, (20)
00BW3886 8	C.BW.00.00BW3886_8	AF443112		2000	Botswana	Novitsky et al., 2002, (20)
00BW3891 6	C.BW.00.00BW3891_6	AF443113		2000	Botswana	Novitsky et al., 2002, (20)
00BW3970 2	C.BW.00.00BW3970_2	AF443114		2000	Botswana	Novitsky et al., 2002, (20)
00BW5031 1	C.BW.00.00BW5031_1	AF443115		2000	Botswana	Novitsky et al., 2002, (20)
01IN565 10	C.IN.99.01IN565_10	AY049708		2001	India	Khurana et al., unpubl.^c
01ZATM45	C.ZA.01.01ZATM45	AY228557		2001	South Africa	Papathanasopoulos et al., 2003, (25)
02YE511	C.YE.02.02YE511	AY795906		2002	Yemen	Saad et al., 2005, (29)
04BR013	C.BR.04.04BR013	AY727522		2004	Brazil	Sanabani et al., 2006, (31)
04BR021	C.BR.04.04BR021	AY727523		2004	Brazil	Sanabani et al., 2006, (31)
04BR038	C.BR.04.04BR038	AY727524		2004	Brazil	Sanabani et al., 2006, (31)
04BR073	C.BR.04.04BR073	AY727525		2004	Brazil	Sanabani et al., 2006, (31)
04BR137	C.BR.04.04BR137	AY727526		2004	Brazil	Sanabani et al., 2006,
04BR142	C.BR.04.04BR142	AY727527		2004	Brazil	Sanabani et al., 2006, (31)
2140707	C.AU.x.2140707	AY857000		--^b	Australia	Kiepiela et al., 2004, (14)
5360558	C.AU.x.5360558	AY857070		--^b	Australia	Kiepiela et al., 2004, (14)
89SM 145	C.SO.x.89SM_145	AY713415		1989	Somalia	Brown et al., 2005, (3)
90SE 364	C.SN.x.90SE_364	AY713416		1990	Sengal	Brown et al., 2005, (3)
92BR025	C.BR.92.92BR025	U52953		1992	Brazil	Gao et al., 1996, (6)
93IN101	C.IN.93.93IN101	AB023804		1993	India	Mochizuki et al., 1999, (17)
93IN904	C.IN.93.93IN904	AF067157		1993	India	Lole et al., 1999, (16)
93IN905	C.IN.93.93IN905	AF067158		1993	India	Lole et al., 1999, (16)
93IN999	C.IN.93.93IN999	AF067154		1993	India	Lole et al., 1999, (16)
94IN11246	C.IN.94.94IN11246	AF067159		1994	India	Lole et al., 1999, (16)
94IN476	C.IN.94.94IN476	AF286223		1994	India	Rodenburg et al., 2001, (27)
95IN21068	C.IN.95.95IN21068	AF067155		1995	India	Lole et al., 1999, (16)
96BW01B03	C.BW.96.96BW01B03	AF110959		1996	Botswana	Novitsky et al., 1999, (21)
96BW0502	C.BW.96.96BW0502	AF110967		1996	Botswana	Novitsky et al., 1999, (21)
96BW06	C.BW.96.96BW06	AF290028		1996	Botswana	Ndung'u et al., 2000, (18)
96BW1104	C.BW.96.96BW1104	AF110969		1996	Botswana	Novitsky et al., 1999, (21)
96BW1210	C.BW.96.96BW1210	AF110972		1996	Botswana	Novitsky et al., 1999, (21)
96BW15C02	C.BW.96.96BW15C02	AF110974		1996	Botswana	Novitsky et al., 1999, (21)
96BW16B01	C.BW.96.96BW16B01	AF110976		1996	Botswana	Novitsky et al., 1999, (21)
96BW17	C.BW.96.96BW17	AF110980		1996	Botswana	Novitsky et al., 1999, (21)
96BWM032	C.BW.96.96BWM032	AF443075		1996	Botswana	Novitsky et al., 2002, (20)
96BWMO1 5	C.BW.96.96BWMO1_5	AF443074		1996	Botswana	Novitsky et al., 2002, (20)
96ZM651	C.ZM.96.96ZM651	AF286224		1996	Zambia	Rodenburg et al., 2001, (27)
96ZM751	C.ZM.96.96ZM751	AF286225		1996	Zambia	Rodenburg et al., 2001, (27)
97TZ04	C.TZ.97.97TZ04	AF361874		1997	Tanzania	Hoelscher et al., 2001, (11)
97TZ05	C.TZ.97.97TZ05	AF361875		1997	Tanzania	Hoelscher et al., 2001, (11)
97ZA003	C.ZA.97.97ZA003	AY118165		1997	Tanzania	Gao, unpubl.^d
97ZA009	C.ZA.97.97ZA009	AY118166		1997	Tanzania	Gao, unpubl.^d
97ZA012	C.ZA.97.97ZA012	AF286227		1997	Tanzania	Rodenburg et al., 2001, (27)
98BR004	C.BR.98.98BR004	AF286228		1998	Brazil	Rodenburg et al., 2001, (27)
98BWMC122	C.BW.98.98BWMC122	AF443076		1998	Botswana	Novitsky et al., 2002, (20)
98BWMC134	C.BW.98.98BWMC134	AF443077		1998	Botswana	Novitsky et al., 2002, (20)
98BWMC14A3	C.BW.98.98BWMC14A3	AF443078		1998	Botswana	Novitsky et al., 2002, (20)
98BWMO1410	C.BW.98.98BWMO1410	AF443079		1998	Botswana	Novitsky et al., 2002, (20)
98BWMO18D5	C.BW.98.98BWMO18D5	AF443080		1998	Botswana	Novitsky et al., 2002, (20)
98BWMO36A5	C.BW.98.98BWMO36A5	AF443081		1998	Botswana	Novitsky et al., 2002,
98BWMO37D5	C.BW.98.98BWMO37D5	AF443082		1998	Botswana	Novitsky et al., 2002, (20)
98IN012	C.IN.98.98IN012	AF286231		1998	India	Rodenburg et al., 2001, (27)
98IN022	C.IN.98.98IN022	AF286232		1998	India	Rodenburg et al., 2001, (27)
98IS002	C.IL.98.98IS002	AF286233		1998	Israel	Rodenburg et al., 2001, (27)
98TZ013	C.TZ.98.98TZ013	AF286234		1998	Tanzania	Rodenburg et al., 2001, (27)
98TZ017	C.TZ.98.98TZ017	AF286235		1998	Tanzania	Rodenburg et al., 2001, (27)
98ZA445	C.ZA.98.98ZA445	AY158533		1998	South Africa	Hunt et al., 2003, (12)
98ZA502	C.ZA.98.98ZA502	AY158534		1998	South Africa	Hunt et al., 2003, (12)
98ZA528	C.ZA.98.98ZA528	AY158535		1998	South Africa	Hunt et al., 2003, (12)
99BW393212	C.BW.99.99BW393212	AF443083		1999	Botswana	Novitsky et al., 2002, (20)
99BW46424	C.BW.99.99BW46424	AF443084		1999	Botswana	Novitsky et al., 2002, (20)
99BW4745	C.BW.99.99BW4745	AF443085		1999	Botswana	Novitsky et al., 2002, (20)
99BW47547	C.BW.99.99BW47547	AF443086		1999	Botswana	Novitsky et al., 2002, (20)
99BWMC168	C.BW.99.99BWMC168	AF443087		1999	Botswana	Novitsky et al., 2002, (20)
99ET1	C.IL.99.99ET1	AY255823		1999	Israel	Harris et al., 2003, (10)
99ET14	C.IL.99.99ET14	AY255825		1999	Israel	Harris et al., 2003, (10)
99ET17	C.IL.99.99ET17	AY255826		1999	Israel	Harris et al., 2003, (10)
99ET7	C.IL.99.99ET7	AY255824		1999	Israel	Harris et al., 2003, (10)
99ZACM9	C.ZA.99.99ZACM9	AF411967		1999	South Africa	Papathanasopoulos et al., 2002, (23)
99ZATM10	C.ZA.99.99ZATM10	AY228556		1999	South Africa	Papathanasopoulos et al., 2003, (24)
A125	C.TZ.01.01TZA125	AY253304		2001	Tanzania	Arroyo et al., 2004, (2)
A207	C.TZ.01.01TZA207	AY253307		2001	Tanzania	Arroyo et al., 2004, (2)
A246	C.TZ.01.01TZA246	AY253308		2001	Tanzania	Arroyo et al., 2004, (2)
A260	C.TZ.01.01TZA260	AY253310		2001	Tanzania	Arroyo et al., 2004, (2)
A301	C.TZ.01.01TZA301	AY253312		2001	Tanzania	Arroyo et al., 2004, (2)
A388	C.TZ.01.01TZA388	AY253317		2001	Tanzania	Arroyo et al., 2004, (2)
A93	C.TZ.01.01TZA93	AY253303		2001	Tanzania	Arroyo et al., 2004, (2)
ARG4006	C.AR.01.ARG4006	AY563170		2001	Argentina	Carrion et al., 2004, (4)
BD16 10	C.TZ.01.01TZBD16_10	AY253320		2001	Tanzania	Arroyo et al., 2004, (2)
BD22 11	C.TZ.01.01TZBD22_11	AY253321		2001	Tanzania	Arroyo et al., 2004, (2)
BD39 8	C.TZ.01.01TZBD39_8	AY253313		2001	Tanzania	Arroyo et al., 2004, (2)
BD9 11	C.TZ.01.01TZBD9_11	AY253322		2001	Tanzania	Arroyo et al., 2004, (2)
CTSC2	C.ZA.99.CTSC2	AY043176		1999	South Africa	von Harmelen et al., 2001, (33)
HIV1084i	C.ZM.x.HIV1084i	AY805330		--^b	Zambia	Grisson et al., 2004, (9)
DU151	C.ZA.99.DU151	AY043173		1999	South Africa	von Harmelen et al., 2001, (33)
DU179	C.ZA.99.DU179	AY043174		1999	South Africa	von Harmelen et al., 2001, (33)
DU422	C.ZA.99.DU422	AY043175		1999	South Africa	von Harmelen et al., 2001, (33)
ETH2220	C.ET.86.ETH2220	U46016		1986	Ethiopia	Salminen et al., 1996, (30)
KER2010	C.KE.00.KER2010	AF457054		2000	Kenya	Dowling et al., 2002, (5)
mIDU101 3	C.MM.99.mIDU101_3	AB097871		1999	Myanmar	Takebe et al., unpubl.^e
TRA3011	C.UY.01.TRA3011	AY563169		2001	Uruguay	Carrion et al., 2004, (4)
TV001	C.ZA.98.TV001	AY162223		1998	South Africa	zur Megede et al., 2002, (34)
TV002	C.ZA.98.TV002	AY162224		1998	South Africa	zur Megede et al., 2002, (34)
TV012	C.ZA.98.TV012	AY162225		1998	South Africa	zur Megede et al., 2002, (34)
ZASW7	C.ZA.99.ZASW7	AF411966		1999	South Africa	Papathanasopoulos et al., 2002, (23)
1069MB	C.ZA.1069MB	AY585268, AY838567	CM	2000	South Africa	Rousseau et al., 2006, (28)
1119MB	C.ZA.1119MB	AY463229	CM	2000	South Africa	Rousseau et al., 2006, (28)
1134MB	C.ZA.1134MB	AY463217	CM	2000	South Africa	Rousseau et al., 2006, (28)
1157M3M	C.ZA.1157M3M	AY585266	CM	2000	South Africa	Rousseau et al., 2006, (28)
1162MB	C.ZA.1162MB	AY463224	CM	2000	South Africa	Rousseau et al., 2006, (28)
1165MB	C.ZA.1165MB	AY463230	CM	2000	South Africa	Rousseau et al., 2006, (28)
1168MB	C.ZA.1168MB	AY463231	CM	2000	South Africa	Rousseau et al., 2006, (28)
1170MB	C.ZA.1170MB	AY463225	CM	2000	South Africa	Rousseau et al., 2006, (28)
1171MB	C.ZA.1171MB	AY463232	CM	2000	South Africa	Rousseau et al., 2006, (28)
1176MB	C.ZA.1176MB	AY463218	CM	2000	South Africa	Rousseau et al., 2006, (28)
1178MB	C.ZA.1178MB	AY463233	CM	2000	South Africa	Rousseau et al., 2006, (28)
1184MB	C.ZA.1184MB	AY585267, AY838566	CM	2000	South Africa	Rousseau et al., 2006, (28)
1189MB	C.ZA.1189MB	AY585264, AY838565	CM	2000	South Africa	Rousseau et al., 2006, (28)
1192M3M	C.ZA.1192M3M	AY463219	CM	2000	South Africa	Rousseau et al., 2006, (28)
1195MB	C.ZA.1195MB	AY463220	CM	2000	South Africa	Rousseau et al., 2006, (28)
1197MB	C.ZA.1197MB	AY463234	CM	2000	South Africa	Rousseau et al., 2006, (28)
1210MB	C.ZA.1210MB	AY463221	CM	2000	South Africa	Rousseau et al., 2006, (28)
1214MB	C.ZA.1214MB	AY463236	CM	2000	South Africa	Rousseau et al., 2006, (28)
1217MB	C.ZA.1217MB	AY463226	CM	2000	South Africa	Rousseau et al., 2006, (28)
1225MB	C.ZA.1225MB	AY463227	CM	2000	South Africa	Rousseau et al., 2006, (28)
1228MB	C.ZA.1228MB	AY463222	CM	2000	South Africa	Rousseau et al., 2006, (28)
2134MB	C.ZA.2134MB	AY463237	CM	2001	South Africa	Rousseau et al., 2006, (28)
J112MA	C.ZA.J112MA	AY585265, AY838568	J	2000	South Africa	Rousseau et al., 2006, (33)
DU422	C.ZA.99.DU422	AY043175		1999	South Africa	von Harmelen et al., 2001, (33)
ETH2220	C.ET.86.ETH2220	U46016		1986	Ethiopia	Salminen et al., 1996, (30)
KER2010	C.KE.00.KER2010	AF457054		2000	Kenya	Dowling et al., 2002, (5)
mIDU101 3	C.MM.99.mIDU101_3	AB097871		1999	Myanmar	Takebe et al., unpubl.^e
TRA3011	C.UY.01.TRA3011	AY563169		2001	Uruguay	Carrion et al., 2004, (4)
TV001	C.ZA.98.TV001	AY162223		1998	South Africa	zur Megede et al., 2002, (34)
TV002	C.ZA.98.TV002	AY162224		1998	South Africa	zur Megede et al., 2002, (34)
TV012	C.ZA.98.TV012	AY162225		1998	South Africa	zur Megede et al., 2002, (34)
ZASW7	C.ZA.99.ZASW7	AF411966		1999	South Africa	Papathanasopoulos et al., 2002, (23)
1069MB	C.ZA.1069MB	AY585268, AY838567	CM	2000	South Africa	Rousseau et al., 2006, (28)
1119MB	C.ZA.1119MB	AY463229	CM	2000	South Africa	Rousseau et al., 2006, (28)
1134MB	C.ZA.1134MB	AY463217	CM	2000	South Africa	Rousseau et al., 2006, (28)
1157M3M	C.ZA.1157M3M	AY585266	CM	2000	South Africa	Rousseau et al., 2006, (28)
1162MB	C.ZA.1162MB	AY463224	CM	2000	South Africa	Rousseau et al., 2006, (28)
1165MB	C.ZA.1165MB	AY463230	CM	2000	South Africa	Rousseau et al., 2006, (28)
1168MB	C.ZA.1168MB	AY463231	CM	2000	South Africa	Rousseau et al., 2006, (28)
1170MB	C.ZA.1170MB	AY463225	CM	2000	South Africa	Rousseau et al., 2006, (28)
1171MB	C.ZA.1171MB	AY463232	CM	2000	South Africa	Rousseau et al., 2006, (28)
1176MB	C.ZA.1176MB	AY463218	CM	2000	South Africa	Rousseau et al., 2006, (28)
1178MB	C.ZA.1178MB	AY463233	CM	2000	South Africa	Rousseau et al., 2006, (28)
1184MB	C.ZA.1184MB	AY585267, AY838566	CM	2000	South Africa	Rousseau et al., 2006, (28)
1189MB	C.ZA.1189MB	AY585264, AY838565	CM	2000	South Africa	Rousseau et al., 2006, (28)
1192M3M	C.ZA.1192M3M	AY463219	CM	2000	South Africa	Rousseau et al., 2006, (28)
1195MB	C.ZA.1195MB	AY463220	CM	2000	South Africa	Rousseau et al., 2006, (28)
1197MB	C.ZA.1197MB	AY463234	CM	2000	South Africa	Rousseau et al., 2006, (28)
1210MB	C.ZA.1210MB	AY463221	CM	2000	South Africa	Rousseau et al., 2006, (28)
1214MB	C.ZA.1214MB	AY463236	CM	2000	South Africa	Rousseau et al., 2006, (28)
1217MB	C.ZA.1217MB	AY463226	CM	2000	South Africa	Rousseau et al., 2006, (28)
1225MB	C.ZA.1225MB	AY463227	CM	2000	South Africa	Rousseau et al., 2006, (28)
1228MB	C.ZA.1228MB	AY463222	CM	2000	South Africa	Rousseau et al., 2006, (28)
2134MB	C.ZA.2134MB	AY463237	CM	2001	South Africa	Rousseau et al., 2006, (28)
J112MA	C.ZA.J112MA	AY585265, AY838568	J	2000	South Africa	Rousseau et al., 2006, (28)
J38MA	C.ZA.J38MA	AY463228	J	2000	South Africa	Rousseau et al., 2006, (28)
J54Ma	C.ZA.J54Ma	AY463223	J	2001	South Africa	Rousseau et al., 2006, (28)
PS077	03ZAPS077B1	DQ093591	PS	2003	South Africa	Rousseau et al., 2006, (28)
PS079	03ZAPS079B1	DQ093592	PS	2003	South Africa	Rousseau et al., 2006, (28)
PS160	04ZAPS160B1	DQ164107	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS161	04ZAPS161B1	DQ164115	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS168	04ZAPS168B1	DQ164121	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS170	04ZAPS170B1	DQ164116	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS188	04ZAPS188B1	DQ164122	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS189	04ZAPS189B1	DQ164117	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS190	04ZAPS190B1	DQ093602	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS193	04ZAPS193B1	DQ164109	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS195	04ZAPS195B1	DQ164118	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS199	04ZAPS199B1	DQ164110	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS201	04ZAPS201B1	DQ164111	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS202	04ZAPS202B1	DQ093598	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS205	04ZAPS205B1	DQ093599	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS208	04ZAPS208B1	DQ093603	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS211	04ZAPS211B1	DQ164112	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS214	04ZAPS214B1	DQ093588	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS216	04ZAPS216B1	DQ093600	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS217	04ZAPS217B1	DQ164119	PS	2004	South Africa	Rousseau et al., 2006, (28)
PS284	04ZAPS284B1	DQ164120	PS	2004	South Africa	Rousseau et al., 2006, (28)
SK005B2	03ZASK005B2	DQ011175	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK006B2	03ZASK006B2	AY878056	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK010	03ZASK008B2	DQ164123	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK011B2	03ZASK010B2	DQ164104	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK019B2	03ZASK019B2	AY878063	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK020B2	03ZASK020B2	AY878064	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK023B2	03ZASK023B2	AY772690	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK026B2	03ZASK026B2	DQ011165	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK029B2	03ZASK029B2	AY772691	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK031B2	04ZASK031B2	AY901974	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK033B2	03ZASK033B2	AY772692	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK034B1	03ZASK034B1	AY878065	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK036B1	03ZASK036B1	AY901966	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK039B2	03ZASK039B2	AY878068	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK040B1	03ZASK040B1	AY703908	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK041B1	03ZASK041B1	AY772693	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK043B1	03ZASK043B1	AY772700	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK058B2	03ZASK058B2	AY901967	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK061B1	03ZASK061B1	AY901968	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK062	03ZASK062B1	DQ164113	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK065B1	03ZASK065B1	AY772694	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK066B1	03ZASK066B1	AY901969	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK072	03ZASK072B1	DQ093593	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK073B1	03ZASK073B1	AY901970	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK076B1	03ZASK076B1	AY901975	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK078B1	03ZASK078B1	AY901971	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK082B1	04ZASK082B1	AY901972	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK083	04ZASK083B2	DQ093585	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK084B1	03ZASK084B1	AY901981	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK092B1	03ZASK092B1	AY878057	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK094B1	03ZASK094B1	AY878070	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK097B1	03ZASK097B1	AY878060	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK098B1	03ZASK098B1	AY878061	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK103	03ZASK103B1	DQ164106	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK107	03ZASK107B1	DQ056410	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK110	03ZASK110B1	DQ056411	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK111	03ZASK111B1	DQ056404	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK112B1	03ZASK112B1	AY772695	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK116B1	03ZASK116B1	AY772696	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK117B1	03ZASK117B1	DQ056408	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK118B1	03ZASK118B1	DQ011169	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK120B1	03ZASK120B1	DQ011176	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK127B1	04ZASK127B1	DQ011172	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK128	04ZASK128B1	DQ093586	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK131	04ZASK131B1	DQ056412	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK132	04ZASK132B1	DQ093594	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK133B1	04ZASK133B1	AY772698	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK134B1	04ZASK134B1	AY703909	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK135B1	04ZASK135B1	DQ011166	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK137	04ZASK137B1	DQ164105	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK139B1	04ZASK139B1	AY878072	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK140B1	04ZASK140B1	AY901973	SK	2004	South Africa	Rousseau et al., 2006,
SK142B1	04ZASK142B1	DQ011167	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK143B1	04ZASK143B1	AY703910	SK	2004	South Africa	Rousseau et al., 2006,
SK144B1	04ZASK144B1	AY703911	SK	2004	South Africa	Rousseau et al., 2006,
SK145B1	04ZASK145B1	AY901976	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK146B1	04ZASK146B1	AY772699	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK147	04ZASK147B1	DQ164114	SK	2004	South Africa	Rousseau et al., 2006,
SK148	04ZASK148B1	DQ093590	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK150B1	04ZASK150B1	DQ011178	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK151B1	04ZASK151B1	AY901977	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK154B1	04ZASK154B1	AY878071	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK155B1	04ZASK155B1	AY901978	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK156B1	04ZASK156B1	DQ011171	SK	2004	South Africa	Rousseau et al., 2006,
SK159B1	04ZASK159B1	DQ011179	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK160B1	04ZASK160B1	DQ011173	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK161B1	04ZASK161B1	DQ011170	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK163B1	04ZASK163B1	AY901979	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK164B1	04ZASK164B1	DQ056405	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK167	04ZASK167B1	DQ164127	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK168B1	04ZASK168B1	AY878058	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK170	04ZASK170B1	DQ093595	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK173	04ZASK173B1	DQ093604	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK174B1	04ZASK174B1	AY901980	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK175	04ZASK175B1	DQ164129	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK176	04ZASK176B1	DQ056416	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK178	04ZASK178B1	DQ093587	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK180B1	04ZASK180B1	AY878059	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK181B1	04ZASK181B1	AY878062	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK182B1	04ZASK182B1	AY878054	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK183B1	04ZASK183B1	AY878055	SK	2004	South Africa	Rousseau et al., 2006,
SK184B1	04ZASK184B1	DQ056418	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK185B1	04ZASK185B1	DQ011174	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK190	04ZASK190B1	DQ056409	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK196	04ZASK196B1	DQ056413	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK202B1	04ZASK202B1	DQ011180	SK	2004	South Africa	Rousseau et al., 2006,
SK204	04ZASK204B1	DQ056414	SK	2004	South Africa	Rousseau
SK206	04ZASK206B1	DQ056415	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK208	04ZASK208B1	DQ056406	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK211	03ZASK211B1	DQ093601	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK212	03ZASK212B1	DQ093596	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK212B	03ZASK212B	DQ978981	SK	2003	South Africa	Present paper
SK213	03ZASK213B1	DQ093607	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK217	04ZASK217B1	DQ056417	SK	2004	South Africa	Rousseau et al., 2006, (28)
SK223	03ZASK223B1	DQ093597	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK226	03ZASK226B1	DQ164108	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK232	03ZASK232B1	DQ093589	SK	2003	South Africa	Rousseau et al., 2006, (28)
SK234	04ZASK234B1	DQ093605	SK	2004	South Africa	Rousseau et al., 2006, (28)

Notes:

a. For Durban, South Africa sequences only: CM: Cato Manor; J: Jeena; PS: Perinatal Study; SK: Sinikethimba Clinic

b. --: sample date unkown

c. We thank Vijay Chaudhary for permission to use unpublished sequence data.

d. We thank Feng Gao for permission to use unpublished sequence data.

e. We thank Shigeru Kasegawa for permission to use unpublished sequence data.

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Table S2: Twenty-three reference sequences

Sequence	Checksum	Name (Accession Number)*
ancD1	2EC7D592	00ZA1210MB (AY463221) 04ZASK139B1 (AY878072)
ancD18	AEC6CE47	99BW46424 (AF443084) 00BW18595 (AF443099)
ancD29	AAE47647	00ZA1171MB (AY463232) 04ZASK170B1 (DQ093595)
ancD33	2062B32B	02YE511 (AY795906) 99ET7 (AY255824)
ancD34	CC3851E7	04ZASK144B1 (AY703911) 04ZASK156B1 (DQ011171)
ancD41	F9E88F14	00ZA1119MB (AY463229) 04ZASK132B1 (DQ093594)
ancT1	70EA53B4	00ZA1195MB (AY463220) 01ZAJ54Ma (AY463223) 03ZAPS077B1 (DQ093591)
ancT2	23B1E2D5	03ZASK020B2 (AY878064) 03ZASK061B1 (AY901968) 04ZAPS170B1 (DQ164116)
ancT8	227B8DAF	01TZA93 (AY253303) 03ZASK232B1 (DQ093589) HIV1084i (AY805330)
ancT13	F771258A	00BW07621 (AF443088) 00BW18802 (AF443100) 99BW47547 (AF443086)
ancT15	2C6BB1E5	01TZBD16 10 (AY253320) 97TZ04 (AF361874) 98TZ017 (AF286235)
ancT16	6CA2549E	99ET1 (AY255823) 99ET14 (AY255825) ETH2220 U46016)
ancT17	D7602B65	96BW17 (AF110980) 00BW147127 (AF443091) 03ZASK029B2 (AY772691)
ancT19	DBC6ED74	03ZASK110B1 (DQ056411) 03ZASK211B1 (DQ093601) 03ZASK006B2 (AY878056)
ancQ3	929ED7F5	99BW393212 (AF443083) 00BW2127214 (AF443105) 00BW38193 (AF443108) KER2010 (AF457054)
ancQ4	E667CCF1	00BW20361 (AF443102) 00BW38428 (AF443109) 04ZASK173B1 (DQ093604) 96BW15C02 (AF110974)
ancQ7	D61168ED	00ZA1168MB (AY463231) 03ZASK116B1 (AY772696) 03ZASK120B1 (DQ011176) 04ZASK131B1 (DQ056412)
ancG10	44B44832	00BW17956 (AF443097) 00BW20636 (AF443103) 96BW1104 (AF110969) 98BWMC134 (AF443077) 96BWMO1 5 (AF443074)
ancIN	D2724A	01IN565 10 (AY049708) 93IN101 AB023804) 93IN904 (AF067157) 93IN905 (AF067158) 93IN999 (AF067154) 94IN11246 (AF067159) 95IN21068 (AF067155) 98IN022 (AF286232) mIDU101 3 AB097871)
ancSAM	C18ABE78	04BR013 (AY727522) 04BR021 (AY727523) 04BR038 (AY727524) 04BR073 (AY727525) 04BR137 (AY727526) 04BR142 (AY727527) 92BR025 U52953) 98BR004 (AF286228) ARG4006 (AY563170) TRA3011 (AY563169)
00BW20872	92F0522C	(AF443104)¹
SK005B2	1BEE86A9	03ZASK005B2 (DQ011175)²
SK213	8226F093	03ZASK213B1 (DQ093607)²

* Names of sequences in clades represented by "anc" sequences, except as below:
¹Accession number for 00BW20872
²Full name and accession number

Downloadable alignments:

nexus

Table S3: Sequences in Recombine analyses

infile1		infile2		infile3		infile4		infile5
name	full name (acc. number)	name	full name (acc. number)	name	full name (acc. number)	name	full name (acc. number)	name	full name (acc. number)
1171MB	00ZA1171MB (AY463232)	00BW21283	00BW21283 (AF443106)	1157M3M	00ZA1157M3M (AY585266)	1069MB	00ZA1069MB (AY838567)	1176MB	00ZA1176MB (AY463218)
BW07621	00BW07621 (AF443088)	1170MB	00ZA1170MB (AY463225)	1225MB	00ZA1225MB (AY463227)	1162MB	00ZA1162MB (AY463224)	1195MB	00ZA1195MB (AY463220)
BW16162	00BW16162 (AF443092)	1189MB	00ZA1189MB (AY838565)	2134MB	01ZA2134MB (AY463237)	BR025	92BR025 (U52953)	2004MB	01ZA2004MB (AY463235)
BW4745	99BW4745 (AF443085)	A246	01TZA246 (AY253308)	A260	01TZA260 (AY253310)	BW1104	96BW1104 (AF110969)	BW15C02	96BW15C02 (AF110974)
BWMO18D5	98BWMO18D5 (AF443080)	BW20636	00BW20636 (AF443103)	BD398	01TZBD39_8 (AY253313)	BW17956	00BW17956 (AF443097)	BW18802	00BW18802 (AF443100)
IN999	93IN999 (AF067154)	BWMC168	99BWMC168 (AF443087)	BE073	04BR073 (AY727525)	BW18595	00BW18595 (AF443099)	BWMC134	98BWMC134 (AF443077)
J112	00ZAJ112MA (AY585265, AY838568)	BWMO1410	98BWMO1410 (AF443079)	BW0402	96BW0402 (AF110962)	BW3886	00BW3886_8 (AF443112)	J38	00ZAJ38MA (AY463228)
PS168	04ZAPS168B1 (DQ164121)	IN904	93IN904 (AF067157)	BW17732	00BW17732 (AF443095)	BW46424	99BW46424 (AF443084)	PS161	04ZAPS161B1 (DQ164115)
SK065B1	03ZASK065B1 (AY772694)	PS170	04ZAPS170B1 (DQ164116)	BW3876	00BW3876_9 (AF443111)	BW47547	99BW47547 (AF443086)	PS201	04ZAPS201B1 (DQ164111)
SK073	03ZASK073B1 (AY901970)	PS189	04ZAPS189B1 (DQ164117)	DU179	C.ZA.99.DU179 (AY043174)	PS190	04ZAPS190B1 (DQ445636, DQ093602)	PS211	04ZAPS211B1 (DQ093606, DQ164112)
SK084	03ZASK084B1 (AY901981)	PS206	04ZASK206B1 (DQ056415)	PS195	04ZAPS195B1 (DQ164118)	PS193	04ZAPS193B1 (DQ164109)	SK010	03ZASK010B2 (DQ164104)
SK128	04ZASK128B1 (DQ093586)	SK040	03ZASK040B1 (AY703908)	PS217	04ZASK217B1 (DQ056417)	SK034	03ZASK034B1 (AY878065)	SK020	03ZASK020B2 (AY878064)
SK133B1	04ZASK133B1 (AY772698)	SK058	03ZASK058B2 (AY901967)	SK078	03ZASK078B1 (AY901971)	SK072	03ZASK072B1 (DQ093593)	SK039	03ZASK039B2 (AY878068)
SK151	04ZASK151B1 (AY901977)	SK062	03ZASK062B1 (DQ164113)	SK092	03ZASK092B1 (AY878057)	SK120	03ZASK120B1 (DQ011176)	SK134	04ZASK134B1 (AY703909)
SK160B1	04ZASK160B1 (DQ011173)	SK139	04ZASK139B1 (AY878072)	SK107	03ZASK107B1 (DQ056410)	SK127	04ZASK127B1 (DQ011172)	SK136	04ZASK136B1 (DQ011177)
SK174	04ZASK174B1 (AY901980)	SK156	04ZASK156B1 (DQ011171)	SK110	03ZASK110B1 (DQ056411)	SK138	04ZASK138B1 (DQ011168)	SK147	04ZASK147B1 (DQ164114)
SK202	04ZASK202B1 (DQ011180)	SK164	04ZASK164B1 (DQ056405)	SK142	04ZASK142B1 (DQ011167)	SK140	04ZASK140B1 (AY901973)	SK181	04ZASK181B1 (AY878062)
SK212	03ZASK212B1 (DQ093596)	SK180	04ZASK180B1 (AY878059)	SK223	03ZASK223B1 (DQ093597)	SK144	04ZASK144B1 (AY703911)	SK182	04ZASK182B1 (AY878054)
TZ.A93	01TZA93 (AY253303)	ZA003	97ZA003 (AY118165)	TV001	TV001 (AY162223)	TV001	TV002 (AY162224)	SK208	04ZASK208B1 (DQ056406)
ZM651	96ZM651 (AF286224)	ZA502	98ZA502 (AY158534)	ZM751	96ZM751 (AF286225)	ZA528	98ZA528 (AY158535)	SK234	04ZASK234B1 (DQ093605)