Rousseau CM, Learn GH, Bhattacharya T, Nickle DC, Heckerman D, Chetty S, Brander C, Goulder PJ, Walker BD, Kiepiela P, Korber BT, Mullins JI 2007 Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. Journal of virology8194492-500 pubmed
Supplemental Data for Rousseau et al. 2007:

Supplemental Figure:
Figure S1: Maximum-likelihood tree of subtype C sequences.

Figure S1: Maximum-likelihood tree of the complete set of subtype C sequences. Outgroup sequences from other subtypes are indicated in gray.

Supplemental Tables:

Table S1 Table S2 Table S3 

Table S1: Sequences used for analyses

Sequence

Full Sequence Name

Accession number

Cohorta

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)
Department of Microbiology
School of Medicine
University of Washington