Table 1 List of 62 HIV-1 reference sequences (including 44 non-recombinant sequences, grouped by subtypes, and 18 circulating recombinant forms (CRFs) included in the study (2005 subtype reference set of the HIV sequence database, Los Alamos National Laboratory).

A1

A1.KE.94.Q23_17.AF004885

J

J.SE.93.SE7887.AF082394

A1.SE.94.SE7253.AF069670

J.SE.94.SE7022.AF082395

A1.UG.92.92UG037.U51190

K

K.CD.97.EQTB11C.AJ249235

A1.UG.98.98UG57136.AF484509

K.CM.96.MP535.AJ249239

A2

A2.CD.97.97CDKTB48.AF286238

O

O.BE.87.ANT70.L20587

A2.CY.94.94CY017_41.AF286237

O.CM.91.MVP5180.L20571

B

B.FR.83.HXB2-LAI-IIIB-BRU.K03455

O.CM.98.98CMU2901.AY169812

B.NL.00.671_00T36.AY423387

O.SN.99.SEMP1300.AJ302647

B.TH.90.BK132.AY173951

N

N.CM.02.DJO0131.AY532635

B.US.98.1058_11.AY331295

N.CM.95.YBF30.AJ006022

C

C.BR.92.BR025-d.U52953

N.CM.97.YBF106.AJ271370

C.ET.86.ETH2220.U46016

C.IN.95.95IN21068.AF067155

CRFs

01_AE.TH.90.CM240.U54771

C.ZA.04.SK164B1.AY772699

02_AG.NG.-.IBNG.L39106

D

D.CD.83.ELI.K03454

03_AB.RU.97.KAL153_2.AF193276

D.CM.01.01CM_4412HAL.AY371157

04_CPX.CY.94.CY032.AF049337

D.TZ.01.A280.AY253311

05_DF.BE.-.VI1310.AF193253

D.UG.94.94UG114.U88824

06_CPX.AU.96.BFP90.AF064699

F1

F1.BE.93.VI850.AF077336

07_BC.CN.97.CN54.AX149771

F1.BR.93.93BR020_1.AF005494

08_BC.CN.97.97CNGX_6F.AY008715

F1.FI.93.FIN9363.AF075703

09_CPX.GH.96.96GH2911.AY093605

F1.FR.96.MP411.AJ249238

10_CD.TZ.96.96TZ_BF061.AF289548

F2

F2.CM.02.02CM_0016BBY.AY371158

11_CPX.GR.-.GR17.AF179368

F2.CM.95.MP255.AJ249236

12_BF.AR.99.ARMA159.AF385936

F2.CM.95.MP257.AJ249237

13_CPX.CM.96.1849.AF460972

F2.CM.97.CM53657.AF377956

14_BG.ES.99.X397.AF423756

G

G.BE.96.DRCBL.AF084936

15_01B.TH.99.99TH_MU2079.AF516184

G.KE.93.HH8793_12_1.AF061641

16_A2D.KR.97.97KR004.AF286239

G.NG.92.92NG083.U88826

18_CPX.CM.97.CM53379.AF377959

G.SE.93.SE6165.AF061642

19_CPX.CU.99.CU38.AY588970

H

H.BE.93.VI991.AF190127

H.BE.93.VI997.AF190128

H.CF.90.056.AF005496