Breakpoints of CRFs
Here we provide breakpoint data for CRFs. For basic descriptions and references, see CRF page.
The breakpoints have been derived from one or more of the following sources, as indicated:
- breakpoints given in publications,
- breakpoints provided in correspondence with the authors,
- analysis of the reference strain with recombination analysis tools (e.g., jpHMM or RIP),
- approximate breakpoints assigned based on published drawings that did not specify exact breakpoints.
CRF01_AE
Breakpoints are approximate, based on Gao et al. 1996 Figure 6.
790 5096 A1 5097 5320 E 5321 5450 A1 5451 5650 E 5651 6310 A1 6311 6500 E/A1 6501 7999 E 8000 8378 E/A1 8379 9085 A1 9086 9600 E
CRF02_AG
Breakpoints from Carr et al. 1998 (exact breakpoints transferred from reference sequence UG037 to HXB2).
1 789 G 790 2155 A 2156 2625 A/G 2626 3274 G 3275 4174 A 4175 4874 G 4875 6224 A/G 6225 8311 A 8312 8588 A/G 8589 9089 A/G 9090 9719 G
CRF03_AB
Breakpoints obtained from jpHMM, in full agreement with map and data in Liitsola et al. 2000.
1 2687 A 2688 8649 B 8650 9719 A
CRF04_cpx
Most breakpoints are approximate, based on figure in Paraskevis et al. 2001; a few breakpoints were taken from jpHMM, but only when those breakpoints agreed with the published figure.
790 1838 A1 1839 2245 G 2876 3717 K 4415 4937 G 4938 5376 A1 5694 6310 A1 6311 6836 G 7510 7793 K 7794 8299 A1 8300 8795 H
CRF05_DF
Approximate breakpoints from Laukkanen et al. 2000; a few breakpoints were taken from jpHMM, but only when those breakpoints agreed with the published results.
790 2291 D 2501 2845 D 2846 3396 F1 3397 3750 D 5191 5700 D 6035 8360 F1 8361 8707 D 8708 9417 F1
CRF06_cpx
Approximate breakpoints from Montavon et al. 2002, with some breakpoints taken from jpHMM.
790 1700 A1 1701 3110 G 3111 3900 K 3901 4266 G 4267 5040 A1 5041 6031 J 6032 8378 G 8379 9417 J
CRF07_BC
Breakpoints from Su, L. et al. 2000 Figure 3 and text descriptions.
790 1269 C 1270 1410 B 1411 2080 C 2081 2620 B 2621 3010 C 3011 3310 B 3311 5699 C 5700 6310 B 6311 8796 C 8797 9058 B 9059 9417 C
CRF08_BC
Breakpoints from Piyasirisilp et al. 2000 Figure 3 and text.
790 1233 C 1234 1680 B 1681 2852 C 2853 3149 B 3150 8796 C 8797 9417 B
CRF09_cpx
Some breakpoints and regional trees for CRF09 are shown in McCutchan et al. 2004. Many regions of the genome have uncertain phylogenetic derivation, so we do not attempt to provide breakpoints or a map.
CRF10_CD
Breakpoints from Koulinska et al. 2001, Figure 1, adding 789 bp to the given coordinates, which begin at gag.
790 3155 D 3156 3216 D/C 3217 3615 C 3616 4316 U 4317 4814 D 4815 4845 D/C 4846 5317 C 5318 5773 D 5774 6340 C 6341 7100 D 7101 7202 C 7203 8883 D 8884 8957 D/C 8958 9442 C
CRF11_cpx
Breakpoints from Montavon et al. 2002 Figure 3 and Figure 4.
790 2090 A 2091 3089 J 3090 3489 U 3490 4039 J 4040 6045 A 6046 6389 J 6390 6789 G 6790 7489 A 7490 7989 U 7990 8653 J 8654 9085 A 9086 9417 E
CRF12_BF
Breakpoints from Carr et al. 2001 as described in text.
739 951 B 952 2981 F1 2473 2640 B 2641 3025 F1 3026 3688 B 3689 5945 F1 5944 6209 B 6210 8482 F1 8483 8660 B 8661 9417 F1
CRF13_cpx
Breakpoints from Zhang et al. 2005 Table 2.
623 2311 G 2312 2453 G/J 2454 3115 J 3116 3163 G/J 3164 4717 G 4718 5096 G/J 5097 6032 J 6033 6283 J/U 6284 6370 U 6371 8215 A1 8216 8396 A1/01_AE 8397 9501 01_AE
CRF14_BG
Breakpoints from Delgado et al. 2002.
750 6322 G 6323 6359 B/G 6360 8260 B 8261 8279 B/G 8280 9500 G
CRF15_01B
Breakpoints from jpHMM, in full agreement with structure shown in Tovanabutra et al. 2003.
790 6308 01_AE 6309 8316 B 8317 9417 01_AE
CRF16_A2D
Breakpoints from Visawapoka et al. 2006.
796 1050 D 1051 2989 A2 2990 3167 D 3168 5510 A2 5511 5850 D 5851 9417 A2
CRF17_BF
Based on RIP analysis of ARMA038 reference sequence.
795 960 B 961 2806 F1 2807 3709 B 3710 5953 F1 5954 6384 B 6385 7683 F1 7684 7840 B 7841 8478 F1 8479 8653 B 8654 9064 F1 9065 9159 B 9169 9603 F1
CRF18_cpx
Breakpoints from Thomson et al. 2005.
795 2080 A 2081 2470 G 2471 2630 U 2631 3040 F 3041 3439 U 3440 3730 A 3761 4130 H 4131 4470 U 4471 4850 G 4851 5710 A/G 5711 6070 K 6071 6300 H 6301 6900 G/J 6920 7750 H 7770 8270 A 8280 8570 H 8790 9442 A
CRF19_cpx
Breakpoints from Casado et al. 2005.
776 1207 A 1208 4239 D 4240 4670 A 4671 5010 G 5011 5290 A 5291 6415 G 6416 8190 A 8191 8510 G 8511 8720 A 8721 9412 D
CRF20_BG
Breakpoints from Sierra et al. 2007.
545 2551 G 2552 2740 B 2741 2974 G 2975 3181 B 3182 3292 G 3293 4148 B 4149 8696 G 8697 8750 B 8751 9488 G
CRF21_A2D
Breakpoints from from Dowling et al. 2002 and Visawapoka et al. 2006.
796 1178 D 1179 1364 A2 1365 3564 D 3565 5510 A2 5511 8639 D 8640 8833 A2 8834 9013 D 9014 9412 A2
CRF22_01A1
Breakpoints from Zhao et al. 2010.
796 2665 01_AE 2666 5452 A1 5453 6723 01_AE 6724 8470 A1 8471 9431 01_AE
CRF23_BG
Breakpoints from Sierra et al. 2007.
571 2551 G 2552 2794 B 2795 2974 G 2975 4148 B 4149 5150 G 5151 5435 B 5436 8696 G 8697 8750 B 8751 9508 G
CRF24_BG
Breakpoints from Sierra et al. 2007.
571 2551 G 2552 2842 B 2843 2974 G 2975 3292 B 3293 3379 G 3380 4148 B 4149 8696 G 8697 8750 B 8751 9508 G
CRF25_cpx
Breakpoints from Yamaguchi et al. 2008.
796 1305 A 1306 3126 G 3127 3690 U 3691 4002 A 4003 5003 G/U 5004 5974 U 5975 6889 G 6890 7665 A 7666 9190 G
CRF26_AU
Breakpoints from M. Peeters.
1 1398 A 1399 1659 U 1660 2378 A 2379 2679 U 2680 4235 A 4236 4514 U 4515 6692 A 6693 6857 U 6858 7969 A 7970 8872 U 8373 9719 A
CRF27_cpx
Breakpoints from author.
803 2151 G 2152 2698 H 2699 2779 U 2780 3986 J 3987 4898 G 4899 5606 J 5607 5986 K 5987 6387 J 6388 8355 01_AE 8356 8659 A 8660 9046 G 9047 9411 H
CRF28_BF
Breakpoints from De Sa Filho et al. 2006.
832 1322 B 1323 2571 F1 2572 9432 B
CRF29_BF
Breakpoints from De Sa Filho et al. 2006.
832 1322 B 1323 2571 F1 2572 3682 B 3683 5462 F1 5463 9432 B
CRF30_0206
N/ACRF31_BC
Breakpoints from Santos et al. 2006.
1 2964 C 2965 2984 B/C 2985 3190 B 3191 3203 B/C 3204 9719 C
CRF32_06A1
Overall structure based on Adojaan et al. 2005; A1 breakpoints determined by jpHMM.
1 789 06_cpx 790 2126 A1 2127 9719 06_cpx
CRF33_01B
Breakpoints from Tee et al. 2006.
634 2052 01_AE 2053 2063 B/01_AE unspecified 2064 2374 B 2375 2416 B/01_AE unspecified 2417 2537 01_AE 2538 2540 B/01_AE unspecified 2541 2840 B 2841 2875 B/01_AE unspecified 2876 9690 01_AE
CRF34_01B
Breakpoints from Tee et al. 2006.
796 2164 01_AE 2165 2679 B 2680 3142 B/01_AE unspecified 3143 8524 01_AE 8525 8749 B 8750 9190 01_AE
CRF35_A1D
Breakpoints from Sanders-Buell et al. 2007.
796 2166 A1 2166 2444 D 2444 2901 A1 2901 3098 D 3098 3184 A1 3184 3378 D 3378 3423 A1 3423 3538 D 3538 7575 A1 7575 7692 D 7692 9190 A1
CRF36_cpx
Breakpoints from Powell et al. 2007b.
796 1929 01_AE 1930 3356 02_AG 3357 4072 A 4073 4305 02_AG 4306 5288 G 5289 6051 02_AG 6080 6253 G 6254 6547 01_AE 6548 7538 A 7539 8368 02_AG 8369 9189 01_AE
CRF37_cpx
Breakpoints from Powell et al. 2007a.
796 1126 01_AE 1126 2142 A 2142 2913 G 2913 4663 A 4663 5120 U 5120 5772 G 5772 6068 U 6068 6431 G 6431 7743 A1 7743 8109 A 8109 8612 02_AG 8612 8873 A 8873 9189 G
CRF38_BF
Breakpoints from Ruchansky et al. 2009.
790 2459 F1 2460 3712 B 3713 9413 F1
CRF39_BF
Breakpoints from Guimaraes et al. 2008.
654 2835 B 2836 3019 F1 3020 3648 B 3649 3865 F1 3866 5677 B 5678 9383 F1
CRF40_BF
Breakpoints from Guimaraes et al. 2008.
654 1339 B 1340 2457 F1 2458 2630 B 2631 3865 F1 3866 4583 B 4584 5036 F1 5037 6563 B 6564 8033 F1 8034 8977 B 8978 9359 F1 9360 9409 B
CRF41_CD
Breakpoints from S. Tovanabutra.
796 1202 D 1203 1463 C 1464 1672 C/D 1673 1857 C 1858 1935 D 1936 2162 C 2163 8326 D 8327 8505 C 8506 9016 D 9017 9510 C
CRF42_BF
Breakpoints from Struck et al. 2015.
767 1433 B 1434 2246 F1 2247 7015 B 7016 7637 F1 7638 9411 B
CRF43_02G
Breakpoints from Yamaguchi et al. 2008.
681 1265 CRF02 1266 3324 G 3325 6096 CRF02 6097 9531 G
CRF44_BF
Breakpoints from the authors.
544 2469 F1 2470 2724 B 2725 2934 F1 2935 3695 B 3696 6341 F1 6342 6446 B 6447 9507 F1
CRF45_cpx
Breakpoints from Niama et al. 2009.
430 2397 A (CRF09-like) 2398 2932 U 2933 3322 K (CRF09-like) 3323 3582 U (K-like) 3583 4079 K 4080 4298 U (CRF04-like) 4299 6041 A 6042 6342 K 6343 8236 A 8237 8604 U (CRF09-like) 8605 9147 A 9148 9515 U
CRF46_BF
Breakpoints from Sanabani et al. 2010.
790 9346 F1 9347 9365 B/F1 9366 9417 B
CRF47_BF
Breakpoints from Fernandez-Garcia et al. 2010.
550 1217 B 1218 1710 F1 1711 1977 B 1978 2397 F1 2398 2567 B 2568 2844 F1 2845 4034 B 4035 4293 F1 4294 4910 B 4911 5805 F1 5806 7000 B 7001 7076 F1 7077 8639 B 8640 8899 F1 8900 8946 B 8947 9350 F1 9351 9507 B
CRF48_01B
Breakpoints from Li et al. 2010.
790 2052 01_AE 2053 2063 01_AE/B 2064 3102 B 3103 3143 01_AE/B 3144 9600 01_AE
CRF49_cpx
Breakpoints from de Silva et al. 2010.
556 789 U 790 2385 A 2386 2395 A/J 2396 2631 J 2632 2652 J/U 2653 2909 U 2910 3001 U/K 3002 3364 K 3365 3381 K/J 3382 3728 J 3729 3758 J/A 3759 4056 A 4057 4108 A/C 4109 5572 C 5573 5730 C/J 5731 9078 J
CRF50_A1D
Breakpoints from Foster et al. 2014.
597 1159 A1 1160 1844 D 1845 2078 A1 2079 2489 D 2490 5979 A1 5980 6551 D 6552 7246 A1 7247 8672 D 8673 9412 A1
CRF51_01B
Breakpoints from Ng et al. 2011.
796 4300 B 4301 5200 01_AE 5201 5800 B 5801 7600 01_AE 7601 8701 B
CRF52_01B
Breakpoints from Liu et al. 2012.
790 2917 01_AE 2918 2941 01_AE/B 2942 3242 B 3243 3259 01_AE/B 3260 6494 01_AE 6495 6546 01_AE/B 6547 8997 B 8998 9010 01_AE/B 9011 9412 01_AE
CRF53_01B
Breakpoints from Chow et al. 2012.
649 2052 01_AE 2053 2063 01_AE/B 2064 2374 B 2375 2422 01_AE/B 2423 9617 01_AE
CRF54_01B
Breakpoints from Ng et al. 2012.
853 990 B 991 1040 01_AE/B 1041 1163 01_AE 1164 1199 01_AE/B 1200 3164 B 3165 3223 01_AE/B 3224 3500 01_AE 3501 3541 01_AE/B 3542 5478 B 5479 5480 01_AE/B 5481 8765 01_AE
CRF55_01B
Breakpoints from Han et al. 2013A.
682 3060 01_AE 3061 3329 B 3330 3767 01_AE 3768 4453 B 4454 9600 01_AE
CRF56_cpx
Breakpoints from Leoz et al. 2013.
760 1053 CRF02 1054 1094 CRF02/B 1095 1170 B 1171 1198 B/G 1199 1332 G 1333 1345 G/CRF02 1346 2654 CRF02 2655 2750 CRF02/B 2751 3177 B 3178 3229 B/CRF02 3230 3327 CRF02 3328 3339 CRF02/B 3340 3819 B 3820 3845 B/CRF02 3846 4071 CRF02 4072 4082 CRF02/B 4083 4137 B 4138 4149 B/CRF02 4150 4417 CRF02 4418 4439 CRF02/B 4440 4776 B 4777 4846 B/CRF02 4847 5751 CRF02 5752 5767 CRF02/G 5768 6365 G 6366 6393 G/B 6394 6980 B 6981 7054 B/CRF02 7055 8210 CRF02 8211 8216 CRF02/B 8217 8340 B 8341 8366 B/CRF02 8367 9417 CRF02
CRF57_BC
Breakpoints from Wei et al. 2014a.
760 1200 C 1201 1225 C/B 1226 1808 B 1809 1863 B/C 1864 9417 C
CRF58_01B
Breakpoints from Chow et al. 2014.
790 2052 01 2053 2095 01/B 2096 2665 B 2666 2689 B/01 2690 3194 01 3195 3259 01/B 3260 3479 B 3480 3524 B/01 3525 7704 01 7705 7742 01/B 7743 8327 B 8328 8384 B/01 8385 9607 01
CRF59_01B
Breakpoints from Han et al. 2013B.
790 2569 CRF01_AE 2570 2718 B 2719 6419 CRF01_AE 6149 8243 B 8244 9600 CRF01_AE
CRF60_BC
Breakpoints from Simonetti et al. 2013.
0 462 B 463 2803 C 2804 3037 B 3038 8661 C 8662 9548 B 9549 9719 C
CRF61_BC
Breakpoints from jpHMM analysis.
790 2789 C 2790 2833 B/C 2834 3130 B 3131 3229 B/C 3230 8748 C 8749 8781 B/C 8782 9062 B 9063 9102 B/C 9103 9412 C
CRF62_BC
Breakpoints from Wei et al. 2014b.
790 2620 C 2621 3219 B 3220 6040 C 6041 6418 B 6419 9598 C
CRF63_02A
Breakpoints from Baryshev et al. 2014.
790 3149 CRF02 3150 3294 CRF02/A1 3295 3922 A1 3923 4139 A1/CRF02 4140 4475 CRF02 4476 4522 CRF02/A1 4523 5148 A1 5149 5155 A1/CRF02 5156 5421 CRF02 5422 5430 CRF02/A1 5431 5555 A1 5556 5582 A1/CRF02 5583 6238 CRF02 6239 6245 CRF02/A1 6246 6349 A1 6350 8805 CRF02 8806 8808 CRF02/A1 8809 9106 A1 9107 9157 A1/CRF02 9158 9626 CRF02
CRF64_BC
Breakpoints from Hsi et al. 2014.
634 1192 C 1193 1332 B 1333 1862 C 1863 2214 B 2215 2370 C 2371 2560 B 2561 4620 C 4621 4870 B 4871 8815 C 8816 9012 B 9013 9602 C
CRF65_cpx
Breakpoints from Feng et al. 2014.
790 1170 01 1171 1197 01/C 1198 3760 C 3761 3801 C/B 3802 4024 B 4025 4105 B/C 4106 5642 C 5643 5655 C/01 5656 5830 01 5831 5869 01/B 5870 5993 B 5994 6008 B/01 6009 6378 01 6379 6397 01/C 6398 7562 C 7563 7587 C/B 7588 8301 B 8302 8330 B/01 8331 8441 01 8442 8498 01/C 8499 8569 C 8570 8586 C/01 8587 8828 01 8829 8995 B 8996 9034 B/C 9035 9613 C
CRF67_01B
Breakpoints from jpHMM, based on sequences from Wu et al. 2013.
790 2966 01_AE 2967 4713 B 4714 9412 01_AE
CRF68_01B
Breakpoints from jpHMM, based on sequences from Wu et al. 2013.
790 2778 01_AE 2779 4852 B 4853 9412 01_AE
CRF69_01B
Breakpoints from Hosaka et al. 2016.
790 1330 CRF01 1331 1482 B 1483 1719 CRF01 1720 4320 B 4321 4568 CRF01 4569 4961 B 4962 5779 CRF01 5780 5911 B 5912 9690 CRF01
CRF70_BF
Breakpoints from Pessoa et al. 2014b, Figure 1.
530 1357 B 1358 1396 B/F1 1397 4008 F1 4009 4020 B/F1 4021 4909 B 4910 4951 B/F1 4952 5362 F1 5363 5395 B/F1 5396 6194 B 6195 6232 B/F1 6233 6257 F1 6258 6449 B/F1 6450 8670 B 8671 8684 B/F1 8685 8870 F1 8871 8893 B/F1 8894 9090 B
CRF71_BF
Breakpoints from Pessoa et al. 2014b, Figure 2.
250 1397 B 1398 4008 F1 4009 4015 B/F1 4016 4898 B 4899 4924 B/F1 4925 5367 F1 5368 5396 B/F1 5397 8659 B 8660 8684 B/F1 8685 8869 F1 8870 8879 B/F1 8880 9531 B
CRF72_BF
Breakpoints from jpHMM analysis of strain MG004 (KJ671535).
790 1359 B 1360 1423 B/F 1424 4287 F 4288 4548 B/F 4549 6506 B 6507 6539 B/F 6540 8231 F 8232 8300 B/F 8301 8624 B 8625 8703 B/F 8704 8868 F 8869 8899 B/F 8900 9411 B
CRF73_BG
Breakpoints from Fernández-García et al. 2016.
790 4579 G 4580 4846 B 4847 5340 G 5341 5514 B 5515 6214 G 6215 8270 B 8271 9420 G
CRF74_01B
Breakpoints from Cheong et al. 2015.
790 2052 01_AE 2053 2063 01_AE/B 2064 2374 B 2375 2416 01_AE/B 2417 2537 01_AE 2538 2551 01_AE/B 2552 2840 B 2841 2875 01_AE/B 2876 3147 01_AE 3148 3160 01_AE/B 3161 3283 B 3284 3325 01_AE/B 3326 9012 01_AE 9013 9038 01_AE/B 9039 9388 B 9389 9606 01_AE
CRF76_01B
Breakpoints from Ogawa et al. 2016.
816 1175 01_AE 1176 1206 01_AE/B 1205 4741 B 4742 4998 01_AE/B 4999 5189 01_AE 5190 5196 01_AE/B 5197 5480 B 5481 5517 01_AE/B 5518 8228 01_AE 8229 8245 01_AE/B 8244 8439 B 8440 8448 01_AE/B 8447 8783 01_AE 8784 8824 01_AE/B 8825 9418 B
CRF78_cpx
Breakpoints from Song et al. 2016.
841 1907 01_AE 1908 2192 B 2193 2671 C 2672 3306 01_AE 3307 3444 C 3445 9530 01_AE
CRF82_cpx
Breakpoints from Chen et al. 2016.
809 1934 C 1935 2021 B 2022 3795 C 3796 4432 B 4433 5678 C 5679 6408 01_AE 6409 8464 C 8465 9124 B
CRF83_cpx
Breakpoints from Chen et al. 2016.
809 1164 01_AE 1165 1911 C 1912 2016 B 2017 2606 C 2607 2694 B 2695 3795 C 3796 4167 B 4168 5734 C 5735 6001 B 6002 8172 01_AE 8173 8538 C 8539 9124 01_AE
CRF85_BC
Breakpoints from Su et al. 2016.
703 2976 C 2977 3106 B 3107 5977 C 5878 6338 B 6339 8863 C 8864 9020 B 9021 9328 C
CRF86_BC
Breakpoints from Li et al. 2016.
841 2637 C 2638 3191 B 3192 3507 C 3508 4532 B 4533 5716 C 5717 6192 B 6193 8497 C 8498 8979 B 8980 9554 C
CRF87_cpx
Breakpoints from Hu et al. 2016.
1 2248 C 2249 2445 B 2446 3123 C 3124 3934 B 3935 4452 C 4453 4800 B 4801 4872 CRF01_AE 4873 5635 C 5636 6057 B 6058 8066 C 8067 8161 CRF01_AE 8162 9719 C
CRF88_BC
Breakpoints from Hu et al. 2016.
1 1178 C 1179 1237 B 1238 1946 C 1947 2094 B 2095 8066 C 8067 8248 B 8249 8417 C 8418 8641 B 8642 9719 C
HIV-2 CRF
HIV2_CRF01_AB
Breakpoints from Ibe et al. 2010.
Note: coordinates are based on HIV-2 reference sequence Mac239.
1 6534 B 6535 6609 A/B 6610 7295 A 7296 7370 A/B 7371 7550 B 7551 7573 A/B 7574 8791 A 8792 8859 A/B 8860 10279 B
