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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:


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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

CRF28_BF

Breakpoints from De Sa Filho et al. 2006.

832 1322 B
1323 2571 F1
2572 9432 B
CRF_image

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
CRF_image

CRF30_0206

N/A

CRF31_BC

Breakpoints from Santos et al. 2006.

1 2964 C
2965 2984 B/C
2985 3190 B
3191 3203 B/C
3204 9719 C
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

CRF38_BF

Breakpoints from Ruchansky et al. 2009.

790 2459 F1
2460 3712 B
3713 9413 F1
CRF_image

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
CRF_image

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
CRF_image

CRF41_CD

Breakpoints from author.

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
CRF_image

CRF42_BF

N/A

CRF43_02G

Breakpoints from Yamaguchi et al. 2008.

681 1265 CRF02
1266 3324 G
3325 6096 CRF02
6097 9531 G
CRF_image

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
CRF_image

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
CRF_image

CRF46_BF

Breakpoints from Sanabani et al. 2010.

790 9346 F1
9347 9365 B/F1
9366 9417 B
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

CRF62_BC

Breakpoints from Wei et al. 2014b.

790 2620 C
2621 3219 B
3220 6040 C
6041 6418 B
6419 9598 C
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

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
CRF_image

 

 


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
CRF_image

 

 

last modified: Thu Jul 17 14:28 2014


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