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).
| Subtype | Sequence name | Subtype | Sequence name |
| 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 |
The last number in each sequence name is the GenBank accession number.