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HIV Circulating Recombinant Forms (CRFs)

This page presents an overview of existing circulating recombinant forms (CRFs).

Select by subtype and or     

Name Reference strain Subtypes Corresponding author #Seqs in SeqDB
(>5000, >100)
HIV-1 CRFs
CRF01_AE CM240 (U54771) A, E J.K. Carr 72026
CRF01_AE represents a putative subtype A/E recombinant that is spreading epidemically in Asia, but originated from Central Africa (Murphy et al. 1993; Carr et al. 1996; Gao et al. 1996). No 'pure' full-length genome has been found for subtype E. In the future, regions of recombinants for which there is no full-length parental strain will be considered unclassified (U). Under the new nomenclature system, CRF01_AE should be referred to as CRF01_AU. But, as the "E" designation for the env region of these strains has been widely used, renaming it would lead to confusion. Thus, the "E" designation has been retained.
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 IbNG (L39106) A, G J.K. Carr 25798
CRF02_AG (Howard and Rasheed 1996) is a subtype A/G recombinant form that is circulating widely in West and Central Africa (Carr et al. 1998), but has also been reported in Taiwan (Lee et al. 1998).
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_A6B Kal153 (AF193276) A6, B K. Liitsola 575
CRF03_A6B represents a subtype A/B recombinant that was first found in Kaliningrad, and is circulating in Russian and Ukrainian cities, primarily in injecting drug users (Liitsola et al. 1998; Lukashov et al. 1999). Circulation of this strain appears to have been accelerated by intravenous injection of a locally produced opiate contaminated with HIV-infected blood. The recombination breakpoints were discussed in detail by Liitsola et al. 2000. CRF03 was reanalyzed by Zarandia et al. 2006 using parental A and B strains (98GEMZ011 and 98GEMZ003) that closely resembled the parental strains that recombined to create CRF03. The use of these parental strains in the analysis revealed an additional segment of subtype A in CRF03 (not shown here).
Breakpoints obtained from jpHMM, in full agreement with map and data in Liitsola et al. 2000.
1 2687 A6
2688 8649 B
8650 9719 A6
CRF04_cpx 94CY032 (AF049337) A, G, H, K, U D. Paraskevis 58
CRF04_cpx (reference strain 94CY032) which represents a Cypriot/Greek recombinant form that was previously classified as an A/G/I recombinant (Gao et al. 1998; Nasioulas et al. 1999). This recombinant has recently been found to be an even more complex mosaic comprised of subtypes A, G, H, K and unclassified regions (Paraskevis et al. 2001). Note that the "I" designation has been dropped from the nomenclature.
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 VI1310 (AF193253) D, F T. Laukkanen 57
The CRF05 chimera was described by Laukkanen et al. 2000, who published 2 genomes (VI1310 and VI961) from Belgian individuals likely infected by partners from the Democratic Republic of the Congo (DRC, former Zaire). A third genome, 99X492(AY227107), was published by Casado et al. 2003.
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 BFP90 (AF064699) A, G, J, K R. B. Oelrichs 3215
The first two full-length sequences of this CRF were BFP90(AF064699) from Burkina Faso (Oelrichs et al. 1998) and 95ML84(AJ245481) from Mali (Montavon et al. 1999). The recombinant was previously named "CRF06_AGJ", but the subsequent identification of subtype K (Triques et al. 2000) suggested that some regions of CRF06 are subtype K, so the subtype is now called "CRF06_cpx". The recombinant structure of the reference sequence was subsequently analyzed by Montavon et al. 2002.
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 97CN54 (AF286226) B, C R. Wagner 17664
A description of this CRF was published by Su et al. 2000 but no sequences were deposited. A patent of the CN54 sequence was recorded with accession numbers AX149771 and AX149647. Two other genomes sequenced by Rodenburg et al. 2001 are available: 97CN001 (AF286226) and 98CN009 (AF286230); however, 97CN001 is reportedly from the same blood sample as CN54. Feng et al. 2016 published an analysis of the orgin and breakpoints of CRF07_BC, CRF08_BC, and other BC-derived CRFs.
Breakpoints from Su 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 97CNGX-6F (AY008715) B, C F.E. McCutchan 3217
The CRF was named by McCutchan 2000. Four near-full-length sequences are available: 97CNGX-6F (AY008715), 97CNGX-7F (AY008716) and 97CNGX-9F (AY008717), all published by Piyasirisilp et al. 2000, and 98CN006 (AF286229) published by Rodenburg et al. 2001. Feng et al. 2016 published an analysis of the orgin and breakpoints of CRF07_BC, CRF08_BC, and other BC-derived CRFs. The CRF09 reference strain was mentioned by McCutchan 2000 and Brodine et al. 2003. The mosaic structure was examined by McCutchan et al. 2004, who provided four complete genomes: 96GH2911 (AY093605), 95SN1795 (AY093603), 99DE4057 (AY093607), and 95SN7808 (AY093604). Their phylogenetic analyses found that most regions of CRF09 cluster most closely with strains of subtypes A or G, and may share some breakpoints with CRF02_AG. However, most regions can best be described as A-like or G-like, as they fall outside the crown group for these subtypes. Some regions appear to be most closely related to strain Z321. Because of the difficulty in assigning many of the regions of CRF09 to any of the pure subtypes, we do not provide a diagram. For more information, see McCutchan et al. 2004. A fifth CRF09 genome was sequenced by Toni et al. 2005: 00IC-10092 (AJ866553).
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 96GH2911 (AY093605) A, G, U F.E. McCutchan 234
The CRF09 reference strain was mentioned by McCutchan 2000 and Brodine et al. 2003. The mosaic structure was examined by McCutchan et al. 2004, who provided four complete genomes: 96GH2911 (AY093605), 95SN1795 (AY093603), 99DE4057 (AY093607), and 95SN7808 (AY093604). Their phylogenetic analyses found that most regions of CRF09 cluster most closely with strains of subtypes A or G, and may share some breakpoints with CRF02_AG. However, most regions can best be described as A-like or G-like, as they fall outside the crown group for these subtypes. Some regions appear to be most closely related to strain Z321. Because of the difficulty in assigning many of the regions of CRF09 to any of the pure subtypes, we do not provide a diagram. For more information, see McCutchan et al. 2004. A fifth CRF09 genome was sequenced by Toni et al. 2005: 00IC-10092 (AJ866553).
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 TZBF061 (AF289548) C, D I.N. Koulinska 260
This CRF was published by Koulinska et al. 2001. Three representatives have been fully sequenced: TZBF061 (AF289548), TZBF071 (AF289549), and TZBF110 (AF289550). Note that some regions of these genomes labeled as subtype D are nearly equidistant between subtypes B and D.
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 GR17 (AF179368) A, E, G, J, U M. Peeters 1388
Six genomes of this CRF are available: GR17 (AF179368) by Paraskevis et al. 2000; MP818 (AJ291718), MP1298 (AJ291719), and MP1307 (AJ291720) by Montavon et al. 2002; and 96CM4496 (AF492623) and 95CM1816 (AF492624) by Wilbe et al. 2002. In the nef/LTR region, both the A and E segments appear to be derived from CRF01_AE, while the other A segments are not. The segments labeled U were regions where the sequence was equidistant between G and J.
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 ARMA159 (AF385936) B, F1 J.K. Carr 532
Four representatives of this CRF, two from Argentina and two from Uruguay, were fully sequenced and described by Carr et al. 2001: AY037279, AF385934, AF385935, and AF385936. Two more complete genomes of this CRF, from Argentina, were described by Thomson et al. 2002: AF408629 and AF408630. Thomson et al. 2000 had previously sequenced the pol region of suspected CRF12_BF isolates (see AF308478..AF308539). Other BF recombinant sequences sharing some but not all recombination sites with CRF12 were also described by Thomson et al. 2002.
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 96CM-1849 (AF460972) CRF01, A, G, J, U K. Wilbe 385
Three representatives of this CRF have been fully sequenced as described by Wilbe et al. 2002 and Kijak et al. 2004: AF460972, AF460974, and AY371154. Regions depicted as derived from "subtype E" here, are derived from CRF01_AE. The J-like region at the gag-pol overlap and into pol, is more closely related to CRF11_cpx than to pure subtype J sequences, while the vif-vpr subtype J region is more closely related to non-recombinant J than to CRF11_cpx. More analysis of this CRF was described by Zhang et al. 2005.
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 X397 (AF423756) B, G R. Najera 337
Six representatives of this CRF, found in Spain, were sequenced by the group of Rafael Najera and described by Delgado et al. 2002: AF423756, AF423757, AF423758, AF423759, AF450096, and AF450097.
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 99TH.MU2079 (AF516184) CRF01, B F.E. McCutchan 60
Four representatives of this CRF, found in Thailand, have been sequenced by the group of Francine McCutchan. The sequence with accession number AF516184 was the first reported to be CRF15_01B. Three more complete genomes have been sequenced and described in Tovanabutra et al. 2003: AF516184, AF529572, AF529573, and AF530576. The genomes of this CRF are derived primarily from CRF01_AE with only the env region (roughly bases 5700 to 7800 in AF516184) being derived from subtype B.
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 97KR004 (AF286239) A2, D U. Visawapoka 57
CRF16 was described by Gomez-Carrillo et al. 2004. Two representative complete genomes of this CRF, found in Kenya and South Korea, plus 2 partial genomes from Argentina, have been sequenced. The sequences KISII5009 (AF457060) and 97KR004 (AF286239) are the complete genomes. Note that AF457060 is hypermutated. Additional analysis of CRF16_A2D and CRF21_A2D was published by Visawapoka et al. 2006.
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_BF1 ARMA038 (AY037281) B, F1 J.K. Carr 17
The structure of ARMA038 (AY037281) was published by Carr et al. 2001. This CRF shares some breakpoints with CRF12_BF. Several related genomes have been sequenced: ARG1139 (EU581825), ARG2233 (EU581826), PSP073 (EU581824), PSP096 (EU581823), BO119 (EU581827), and PCR155 (EU581828).
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 CU76 (AY586540) A1, F, G, H, K, U M. Thomson 331
CRF18 was described by Thomson et al. 2005, who provided two genome sequences, CU76 (AY586540) and CU14 (AY586541). Other genome sequences include CU68 (AY894993) and CM53379 (AF377959). In the drawing, the ambiguous region around 5280 was rooted between A and G, and the region around 6600 was rooted between G and J.
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 CU7 (AY894994) A1, D, G M. Thomson 784
CRF19 was described by Casado et al. 2005, who provided three genome sequences, AY894994, AY588970, and AY588971.
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 Cu103 (AY586545) B, G M. Thomson 260
Perez et al. 2006 described 3 clusters of BG recombinant sequences found among HIV patients in Cuba. Sierra et al. 2007 determined the breakpoints of these recombinants and defined them as CRFs 20, 23, and 24. Genome sequences for CRF20 include: Cu103 (AY586545), R77 (AY586544), and CB134 (DQ020274).
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 99KE_KER2003 (AF457051) A2, D F.E. McCutchan 14
CRF21 was described by Dowling et al. 2002. Genome sequences include: AF457051 and AF457072. Additional analysis of CRF16_A2D and CRF21_A2D was published by Visawapoka et al. 2006.
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 02CMLT72 (EU743963) CRF01, A1 J.K. Carr 220
Carr et al. 2001 published an analysis of a novel URF, CM53122 (AY037284 + AY037285), which was a recombinant of CRF01_AE and segments of subtype A1 that were not derived from CRF01. The authors later defined this as a CRF, based on two genome sequences, CM3097 (GQ229529) and CM001BBY (AY371159). Zhao et al. 2010 published documentation of the CRF22 mosaic structures of several genomes, and classified CM53122 as a URF containing segments of CRF01 and CRF22. They selected 02CMLT72 (EU743963) as the reference strain. Zhao et al. 2012 documented additional CRF22 genomes and CRF22 recombinants with other subtypes and CRFs.
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 CB118 (AY900571) B, G M. Thomson 29
Perez et al. 2006 described 3 clusters of BG recombinant sequences found among HIV patients in Cuba. Sierra et al. 2007 determined the breakpoints of these recombinants and defined them as CRFs 20, 23, and 24. Genome sequences for CRF23 include CB118 (AY900571) and CB347 (AY900572).
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 CB378 (AY900574) B, G M. Thomson 90
Perez et al. 2006 described 3 clusters of BG recombinant sequences found among HIV patients in Cuba. Sierra et al. 2007 determined the breakpoints of these recombinants and defined them as CRFs 20, 23, and 24. Genome sequences for CRF24 include CB378 (AY900574), CB619 (AY900576), CB471 (AY900575), CB228 (AY900577), and CB219 (AY900581).
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 1918LE (AY371169) A, G, U J.K. Carr 156
CRF25_cpx was first described in unpublished data by J. Carr: 01CM.101BA (DQ826726). A second complete genome of CRF25 was identified by Kijak et al. 2004: 02CM_1918LE (AY371169). A third genome from Cameroon was identified by Luk et al. 2008: BA040 (EU693240). Two complete genomes from Saudi Arabia were described by Yamaguchi et al. 2008: J11233 (EU697906) and J11451 (EU697908).
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_A5U 02CD_MBTB047 (FM877782) A, U M. Peeters 43
CRF26_A5U was described by Vidal et al. 2009 with 4 complete genomes: 02CD_KS069 (FM877780), 97CD_KTB119 (FM877777), 02CD_LBTB084 (FM877781), and 02CD_MBTB047 (FM877782). The authors showed that the A regions of these genomes cluster separately from other A sub-subtypes, and so defined this novel cluster as sub-subtype A5.
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 04FR-KZS (AM851091) A, E, G, H, J, K, U M. Peeters 20
Vidal et al. 2008 defined CRF27 based on 3 epidemiologically unlinked genome sequences, 2 from the Democratic Republic of Congo and 1 from a Congolese patient sampled in France: 97CD-KTB49 (AJ404325), 02CD-LBR024 (AM851090), and 04FR-KZS (AM851091).
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_BF1 BREPM12609 (DQ085873) B, F1 R. Diaz 13
CRF28 and CRF29 were described by De Sa Filho et al. 2006 and Sanabani et al. 2006. CRF28 genome sequences include: DQ085873, DQ085874, and DQ085872.
Breakpoints from De Sa Filho et al. 2006.
832 1322 B
1323 2571 F1
2572 9432 B
CRF29_BF1 BREPM16704 (DQ085876) B, F1 R. Diaz 14
CRF28 and CRF29 were described by De Sa Filho et al. 2006 and Sanabani et al. 2006. CRF29 genome sequences include: DQ085876, AY455778, and DQ085871. Three complete genomes, each recombinant between CRF02_AG and CRF06_cpx, were described by S. Mamadou et al. 2003, However, 3 complete genomes of the same form have not yet been sequenced. Each of these three genomes, NE03 (AJ508595), NE95 (AJ508596), and NE36 (AJ508597), has a different set of recombination breakpoints. A fourth genome, 0303GH195 (AB286854), also has a different CRF02/CRF06 recombination structure, although it is closest to NE03, perhaps sharing two or more of the same sites of recombination.
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 00NE36 (AJ508597) CRF02, CRF06 M. Peeters 5

CRF31_BC 04BR142 (AY727527) B, C M. Soares 70
CRF31 was described by Santos et al. 2006. Complete genomes include 04BR137 (AY727526), 04BR142 (AY727527), and 110PA (EF091932), all from Brazil.
Breakpoints from Santos et al. 2006.
1 2964 C
2965 2984 B/C
2985 3190 B
3191 3203 B/C
3204 9719 C
CRF32_06A6 EE0369 (AY535660) CRF06, A6 M. Adojaan 6
CRF32 was described by Adojaan & Kivisild 2005, who provided reference sequence EE0369 (AY535660) and another CRF06/A1 recombinant EST2002_1169 (DQ167215).
Overall structure based on Adojaan & Kivisild 2005; A1 breakpoints determined by jpHMM.
1 789 06_cpx
790 2126 A1
2127 9719 06_cpx
CRF33_01B 05MYKL007 (DQ366659) CRF01, B K.P. Ng & K.K. Tee 248
CRF33 was described by Tee et al. 2006, who provided 4 genome sequences from Malaysia: 05MYKL007_1 (DQ366659), 05MYKL015_2 (DQ366660), 05MYKL031_1 (DQ366661), and 05MYKL045_1 (DQ366662). Hu et al. 2016 identified an additional genome sequence of CRF33, 07MYKLD47 (EU031913).
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 OUR2275P (EF165540) CRF01, B F.E. McCutchan 10
CRF34 was described by Tovanabutra et al. 2007 based on 3 genome sequences from Thailand: OUR1969P (EF165539), OUR2275P (EF165540), and OUR2478P (EF165541).
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 AF095 (EF158041) A1, D F.E. McCutchan 1560
CRF35 was described by Sanders-Buell et al. 2007 based on 4 genome sequences from Afghanistan: AF094 (EF158040), AF095 (EF158041), AF104 (EF158042) and AF026 (EF158043).
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 NYU830 (EF087994) CRF01, CRF02, A, G R. Powell 27
CRF36 was described by Powell et al. 2007b based on 2 genome sequences from Cameroon: NYU830 (EF087994) and NYU1162 (EF087995). Two regions of CRF36 were found to cluster significantly with CRF22.
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 NYU926 (EF116594) CRF01, CRF02, A, G, U R. Powell 136
CRF37 was described by Powell et al. 2007a based on 2 genome sequences from Cameroon: NYU926 (EF116594) and CM53392 (AF377957). Parts of CRF37 cluster very closely with CRF19.
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_BF1 UY03_3389 (FJ213783) B, F1 C. Lopez-Galindez 5
CRF38 was described by Ruchansky et al. 2009 based on 4 genomes from Uruguay: UY03_3389, UY04_4022, UY05_4752, and UY04_3987 (accessions FJ213780-FJ213783). CRF38 shares two breakpoints in Pol with CRF12_BF.
Breakpoints from Ruchansky et al. 2009.
790 2459 F1
2460 3712 B
3713 9413 F1
CRF39_BF1 03BRRJ103 (EU735534) B, F1 M.G. Morgado 8
Guimaraes et al. 2008 described two BF1 recombinants in Brazil, CRF39 and CRF40. CRF39 was defined based on 3 genome sequences: 03BRRJ103 (EU735534), 04BRRJ179 (EU735535) and 03BRRJ327 (EU735536).
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_BF1 05BRRJ055 (EU735537) B, F1 M.G. Morgado 6
Guimaraes et al. 2008 described two BF1 recombinants in Brazil, CRF39 and CRF40. CRF40 was defined based on 4 genome sequences: 05BRRJ055 (EU735537), 04BRRJ115 (EU735538), 05BRRJ200 (EU735539) and 04BRSQ46 (EU735540).
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 CO6650V1 (KX907417) C, D S. Tovanabutra 5
CRF41_CD was described by Billings et al. 2017. It is based on 3 genomes: CO6577V5 (KX907411), CO6650V1 (KX907417), and CO6952V1 (KX907430).
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_BF1 luBF_13_05 (EU170136) B, F1 J-C. Schmit 61
CRF42_BF was described by Struck et al. 2015. There were 21 complete genomes sequenced, with accession numbers EU170135-EU170155. The study also identified genome fragments matching CRF42 among sequences from Brazil, France and Belgium.
Breakpoints from Struck et al. 2015.
767 1433 B
1434 2246 F1
2247 7015 B
7016 7637 F1
7638 9411 B
CRF43_02G J11223 (EU697904) CRF02, G C. Brennan 33
Yamaguchi et al. 2008 described 4 complete genomes from Saudi Arabia: J11223 (EU697904), J11232 (EU697905), J11243 (EU697907), and J11456 (EU697909).
Breakpoints from Yamaguchi et al. 2008.
681 1265 CRF02
1266 3324 G
3325 6096 CRF02
6097 9531 G
CRF44_BF1 CH80 (FJ358521) B, F1 M. Thomson 21
CRF44_BF was noted in Rios et al. 2007 as a group of related sequences with shared breakpoints. The related genome CH12 (AY536235) had been previously sequenced by Sierra et al. 2005, and the epidemiologically unlinked CH80 (FJ358521) genome was subsequently sequenced by Delgado et al. 2010. The pol reverse transcriptase sequences from 10 CRF44 isolates in the Rios 2007 paper are: EF193891, EF193892, EF193912, EF193945, EF193954, EF193979, EF193986, EF194007, EF194024 and EF200123.
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 04FR.AKU (EU448295) A, K, U M. Peeters 148
CRF45 was described by Niama et al. 2009. They identified genome sequence 04FR.AKU (EU448295) and 4 additional genomes (FN392874-FN392877) from multiple countries. Some fragments of CRF45 resemble regions of CRF04_cpx or CRF09_cpx. CRF45 may be the ancestral lineage of complex recombinants HIV-MAL and HIV-NOGIL. Delatorre et al. 2016 characterized genomes of CRF45 from Brazil.
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_BF1 01BR087 (DQ358801) B, F1 S. S. Sanabani 8
CRF46 was described by Sanabani et al. 2010. They provided 5 genome sequences (HM026456-HM026460) and identified a previously-published sequence 01BR087 (DQ358801) as CRF46. They also noted several other genomes with the same breakpoint pattern, but evolutionarily distinct.
Breakpoints from Sanabani et al. 2010.
790 9346 F1
9347 9365 B/F1
9366 9417 B
CRF47_BF1 P1942 (GQ372987) B, F1 M. Thomson 24
CRF47 was described by Fernandez-Garcia et al. 2010. They provided 2 genome sequences, P1942 (GQ372987) and X2457 (FJ670529), plus additional pol sequences, all from patients in Spain. This is the first B/F1 CRF to be identified outside of South America. The subtype F segments are distinct from South American subtype F1 sequences.
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 07MYKT014 (GQ175881) CRF01, B Y. Takebe 24
CRF48 was described by Li et al. 2010. They provided 3 genome sequences and additional partial sequences from Malaysian patients in an IVDU cohort (GQ175881-GQ175903). CRF48 shares one breakpoint with CRF33_01B. Phylogenetic analysis and estimates of most recent common ancestor indicate that CRF48 is likely to be a descendent of CRF33.
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 N28353 (HQ385478) A1, C, J, K, U T. de Silva & M. Cotten 34
CRF49 was described by de Silva et al. 2010. They provided 3 genome sequences from Gambian patients N018380, N026677, and N28353 (HQ385477-HQ385479), plus env/gag gene pairs from 3 more isolates: N001605 (HQ385466, HQ385480), N005284 (HQ385443, HQ385481), and N024017 (HQ385461, HQ385482).
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 8179 (JN417236) A1, D G. Foster 6
CRF51 was described by Foster et al. 2014. They provided 5 genome sequences from MSM in the UK (JN417236, JN417237, JN417239, JN417240, JN417241).
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 HM021 (JN029801) CRF01, B O.T. Ng 82
CRF51 was described by Ng et al. 2011. They provided 3 genome sequences from patients in Singapore: HM021, HM062, and HM091 (JN029801-JN029803). Jagdagsuren et al. 2017 sequenced 3 CRF51 genomes in Mongolia. CRF52 was described by Liu et al. 2012. It was the first CRF to be identified based on previously-published genome sequences that were already present in sequence databases. These sequences are: M043 from Thailand (DQ354113), MYKL018 from Malaysia (DQ366664), and R1741 from Thailand (AY945734).
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 M043 (DQ354113) CRF01, B J. Li 8

Breakpoints from Liu et al. 2012.
790 2917 01_AE
2918 2941 01_AE/B
2942 3242 B
3243 3259 01_AE/B
3260 8494 01_AE
8495 8546 01_AE/B
8547 8997 B
8998 9010 01_AE/B
9011 9412 01_AE
CRF53_01B 11FIR164 (JX390610) CRF01, B K.K. Tee 9
CRF53 was described by Chow et al. 2012. They provided 3 genome sequences from patients in Malaysia: 11FIR164, 10MYKJ079, and 10MYKJ067 (JX390610-JX390612). They also identified previously-published 04MYKL016 (DQ366663) as a member of this CRF. Maximum likelihood analysis of subgenomic regions revealed that CRF53_01B is closely related to CRF33_01B and is likely to be the ancestor of CRF33_01B, which may have emerged in the early 1990s.
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 09MYSB023 (JX390976) CRF01, B K.K. Tee 15
CRF54 was described by Ng et al. 2012. They provided 2 genome sequences from patients in Malaysia: 09MYSB023 and 08MYKL044 (JX390976-JX390977). They also identified previously-published 07MYKLD49 (EU031915) as a member of this CRF.
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 HNCS102056 (JX574661) CRF01, B X. Han 2222
CRF55 was described by Han et al. 2013A. They provided 3 genome sequences from MSM patients in two different regions of China: HNCS102056, GDD318, GDD095 (JX574661-JX574663). The authors noted that the subtype B regions of this recombinant are related to Western strains, not the Thai B' variant, while the CRF01 regions are related to Thai strains of CRF01, not those found in other MSM in China. Han et al. 2015 conducted a large-scale survey of CRF55 among MSM in China and sequenced additional genomes.
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 URF5 (JN882655) CRF02, B, G M. Leoz 11
CRF56 was described by Leoz et al. 2013. They presented 4 genome sequences from unlinked MSM in Paris, France. Colson et al. 2014 identified additional pol sequences from France and the Philippines that cluster with CRF56.
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 1439 (JX679207) B, C L. Li 36
CRF57 was described as "Cluster III" by Li et al. 2012. They provided the genome sequence from isolate 1439 (JX679207), which had the same recombinant pattern as isolate 341 (HM776939) from a previous study. An additional CRF57 genome sequences was identified by Han et al. 2013 (KC899008). A full description of CRF57, together with 2 additional genome sequences, was provided by Wei et al. 2014a (KC870044, KF250400).
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 09MYPR37 (KC522031) CRF01, B K.K. Tee 10
CRF58 was described by Chow et al. 2014. They provided 6 genome sequences from IV drug users in Malaysia (KC522031-KC522035, KF425293). CRF58 shares unique recombination breakpoints with other established CRFs in the region: CRF33_01B, CRF48_01B, and CRF53_01B in the gag gene, and CRF15_01B in the env gene.
Breakpoints from Chow et al. 2014.
790 2052 01_AE
2053 2095 01_AE/B
2096 2665 B
2666 2689 B/01_AE
2690 3194 01_AE
3195 3259 01_AE/B
3260 3479 B
3480 3524 B/01_AE
3525 7704 01_AE
7705 7742 01_AE/B
7743 8327 B
8328 8384 B/01_AE
8385 9607 01_AE
CRF59_01B 09LNA423 (JX960635) CRF01, B X. Han 124
CRF59 was described by Han et al. 2013B. They provided 3 genome sequences from unlinked MSM patients: KC462190, KC462191, and JX960635. CRF59 is the second 01B CRF identified in the MSM population in China: CRF55 was identified among MSM in southern China, while CRF59 was identified among MSM in northeastern China. Additional genome sequences were published by Zhang et al. 2014 and Hu et al. 2016.
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 BAV499 (KC899079) B, C F. Simonetti 189
CRF60 was described by Simonetti et al. 2013. They provided 3 genome sequences from unlinked patients from Italy: KC899079-KC899081.
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 JL100010 (KC990124) B, C X. Li 6
CRF61 was described by Li et al. 2013. They provided 3 genome sequences from unlinked patients in China: KC990124-KC990126. CRF61 may have originated from two established recombinants, CRF07_BC and CRF08_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 YNFL13 (KC870034) B, C Yiming Shao 5
CRF62 was described by Wei et al. 2014b. They provided 3 genome sequences from unlinked patients in Dehong Prefecture, Yunnan, China (KC870034, KC870035, KC870037).
Breakpoints from Wei et al. 2014b.
790 2620 C
2621 3219 B
3220 6040 C
6041 6418 B
6419 9598 C
CRF63_02A6 10RU6637 (JN230353) CRF02, A6 P. Baryshev 1695
CRF63 was described by Baryshev et al. 2014, who identified 8 genome sequences from Russia (JN230353, JX500698-JX500705). Shcherbakova et al. 2014 provided additional analysis of the epidemiology, phylogeny, and phylodynamics CRF63.
Breakpoints from Baryshev et al. 2014.
790 3149 CRF02
3150 3294 CRF02/A6
3295 3922 A6
3923 4139 A6/CRF02
4140 4475 CRF02
4476 4522 CRF02/A6
4523 5148 A6
5149 5155 A6/CRF02
5156 5421 CRF02
5422 5430 CRF02/A6
5431 5555 A6
5556 5582 A6/CRF02
5583 6238 CRF02
6239 6245 CRF02/A6
6246 6349 A6
6350 8805 CRF02
8806 8808 CRF02/A6
8809 9106 A6
9107 9157 A6/CRF02
9158 9626 CRF02
CRF64_BC YNFL31 (KC870042) B, C Yiming Shao 17
CRF64 was described by Hsi et al. 2014. They provided 6 genome sequences from 5 unlinked patients in Dehong Prefecture, Yunnan, China (KC870032, KC870036, KC870040, KC870042, KC870043). Hu et al. 2016 identified 3 additional genome sequences of CRF64.
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 YNFL05 (KC870030) CRF01, B, C Yiming Shao 48
CRF65 was described by Feng et al. 2014, who provided 4 genome sequences (KC183778, KC870027, KC870028, KC870030).
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
CRF66_BF1 02PY-PSP0093 (JN251902) B, F1 Michael Thomson 26
CRF66 was described by Michael Thomson, based on 3 complete genomes MK298150 from Spain and JN251902 and JN251903 from Paraguay, but has not yet been published.
Breakpoints from jpHMM, based on correspondence from Michael Thomson, as yet unpublished.
1 559 U
560 978 B
979 4307 F1
4308 6530 B
6531 8481 F1
8482 9254 B
9255 9489 F1
9489 9719 U
CRF67_01B MAS59 (KC183780) CRF01, B Jianjun Wu 93
CRF67 was described by Wu et al. 2013. It was not named as CRF67_01B in that paper, but was described as part of a group of sequences with similar breakpoints. Later analyses proved that the sequences represented by triangles in figure 3 of this paper represented two different forms (CRF67 and CRF68).
Breakpoints from jpHMM, based on sequences from Wu et al. 2013.
790 2966 01_AE
2967 4713 B
4714 9412 01_AE
CRF68_01B XC46 (KC183783) CRF01, B Jianjun Wu 68
CRF68 was described by Wu et al. 2013. It was not named as CRF68_01B in that paper, but was described as part of a group of sequences with similar breakpoints. Later analyses proved that the sequences represented by triangles in figure 3 of this paper represented two different forms (CRF67 and CRF68). A genome was also described by Guo et al. 2014.
Breakpoints from jpHMM, based on sequences from Wu et al. 2013.
790 2778 01_AE
2779 4852 B
4853 9412 01_AE
CRF69_01B 10JP-5091N200 (AB845349) CRF01, B J. Hattori 7
CRF69_01B was first described in conference proceedings (Hosaka et al. 2014. CRF01_AE and subtype B transmission networks cross over: a new AE-B recombinant emerges in Japan. Abstr. 21st Conf. Retroviruses Opportunistic Infections, abstr B-229). Subsequently, a genome with the same breakpoints was identifed by Kusagawa et al. 2015 (LC027100). Six additional genomes were published by Hosaka et al. 2016.
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_BF1 PE004 (KJ849758) B, F1 R. Pessoa 7
Pessoa et al. 2014b identified CRF70 and CRF71 among blood donors in Pernambuco, Brazil. CRF70 was documented with 4 near-full-length genomes.
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_BF1 PE008 (KJ849759) B, F1 R. Pessoa 25
Pessoa et al. 2014b identified CRF70 and CRF71 among blood donors in Pernambuco, Brazil. CRF71 was documented with 12 near-full-length genomes.
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_BF1 MG002 (KJ671534) B, F1 S. Sanabani 7
CRF72 was described by Pessoa et al. 2014a, who provided 5 genome sequences (KJ671533-KJ671537).
Breakpoints from jpHMM analysis of strain MG004 (KJ671535).
790 1359 B
1360 1423 B/F1
1424 4287 F1
4288 4548 B/F1
4549 6506 B
6507 6539 B/F1
6540 8231 F1
8232 8300 B/F1
8301 8624 B
8625 8703 B/F1
8704 8868 F1
8869 8899 B/F1
8900 9411 B
CRF73_BG 9196_01 (AY882421) B, G M. Thomson 9
CRF73 was described by Fernández-García et al. 2016, who identified 2 genomes (AY882421 KM248765) and several partial genomes with a common set of breakpoints.
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 10MYPR268 (KR019771) CRF01, B K.K. Tee 13
CRF74 was described by Cheong et al. 2015, who provided 3 genome sequences from Malaysia (KR019770-KR019772). CRF74 appears to be closely related to CRF33_01B and CRF53_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
CRF75_BF1 58736 (GU595160) B, F1 M. Thomson 9
CRF75 is unpublished, by Michael Thomson, who provided 4 genome sequences MK341078, GU595149, GU595157 and GU595160. Three of these genomes were published by Saladini et al. 2012 showing different recombination breakpoints, but Michael Thomson grouped them together as one CRF based on phylogeny.
CRF75 is unpublished but was defined by Michael Thomson.
517  1242  B
1243  3179  F1
3180  3416  B
3417  3575  F1
3576  3721  B
3722  4326  F1
4327  4487  B
4488  4537  F1
4538  4775  B
4776  5233  F1
5234  5641  B
5642  5777  F1
5778  6477  B
6478  6564  F1
6565  6809  B
6810  7094  F1
7095  7569  B
7570  7804  F1
7805  8683  B
8684  9019  F1
9019  9466  B
CRF76_01B N628 (MN187303) CRF01, B A. Hachiya 6
CRF76 was described by Ogawa et al. 2016, based on sequences from Japan. In addition to NGS sequences, two genome sequences were published (MN187302, MN187303).
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
CRF77_cpx 14MYNBB090 (KX673820) CRF01, B, C K.K. Tee 4
CRF77 was described by Tee et al. 2017, who provided 4 near-full length sequences (KX673818-KX673821). It was found among blood donors in Malaysia.
Breakpoints from Tee et al. 2017.
708 1197 C
1198 1244 B/C
1245 1356 B
1357 1379 B/C
1380 1557 C
1558 1562 B/C
1563 1636 B
1637 1690 B/C
1691 1962 C
1963 1970 B/C
1971 2100 B
2101 2132 B/C
2133 2987 C
2988 3031 B/C
3032 3164 B
3165 3205 B/C
3206 4739 C
4740 4987 C/CRF01
4988 8765 CRF01
8766 8783 C/CRF01
8784 9569 C
CRF78_cpx YNTC19 (KU161143) CRF01, B, C X. Xia 5
CRF78 was described by Song et al. 2016, who provided 3 genome sequences from Yunnan, China (KU161143-KU161145).
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
CRF79_0107 SX15DT013 (KY216146) CRF01, CRF07 Yiming Shao 35
CRF79 was described by Li et al. 2017, who provided 3 near-full length sequences (KY216146-KY216148). All were from Shanxi Province of China with risk factors of heterosexual and MSM transmission.
Breakpoints from Li et al. 2017.
790 4328 CRF01
4329 4808 CRF07
4809 6559 CRF01
6560 8592 CRF07
8593 9095 CRF01
9096 9411 CRF07
CRF80_0107 YA285 (MH843712) CRF01, CRF07 Y. Zhang 3
CRF80 was described by Zhang et al. 2018, who provided 2 near-full length sequences (MH843712 and MH843713), and noted that KX198573 shared the same recombination breakpoints. Two were from Beijing China with risk factors of MSM transmission, and KX198753 was from Hebei with risk factor also MSM.
Breakpoints from Zhang et al. 2018.
1 789 U
790 2411  CRF01_AE
2412  3472  CRF07_BC
3473  5038  CRF01_AE
5039  5647  CRF07_BC
5648  6396  CRF01_AE
6397  8434  CRF07_BC
8435  8828  CRF01_AE
8829  9411  CRF07_BC
9412  9719   U
CRF81_cpx BRGO3001 (MH986016) B, C, F1 Monica N. G. Reis 6
CRF81 was described by Reis et al. 2019, who provided 2 near-full length sequences (accession numbers pending), and noted that accession number pending shared the same recombination breakpoints. KX888281, KX281891, KM851055 and KM851122 also seem to belong to this CRF.
Breakpoints from Reis et al. 2019.
1 625 U
626 1196  B
1197  2611  F1
2612  2962  C
2963  3675  B
3676  5135  F1
5136  5924  C
5925  6224  B
6225  8079  C
8080  8825  B
8826  9321  C
9322  9719  U
CRF82_cpx mSSDU12 (KU820825) CRF01, B, C Xin Chen 6
CRF82 was described by Chen et al. 2017, who provided 6 near-full length sequences from intravenous drug users in Myanmar.
Breakpoints from Chen et al. 2017.
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 mSSDU94 (KU820847) CRF01, B, C Xin Chen 14
CRF83 was described by Chen et al. 2017, who provided 11 near-full length sequences from intravenous drug users in Myanmar.
Breakpoints from Chen et al. 2017.
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
CRF84_A1D NFLG088SE (MF373190) A1, D Ujjwal Neogi 3

Breakpoints from Neogi et al. 2017.
0 789 U
790 2808 A1
2809 4168 D
4169 5326 A1
5327 7015 D
7016 7229 A1
7630 8566 D
8567 9406 A1
9407 9719 U
CRF85_BC SCYB2 (KU992929) B, C S. Liang 176
CRF84_DG was not fully classified as a CRF because the sequences instead turned out fo be similar but unique recombinants. Neogi et al. 2017. The A1/D recombinants have accession numbers MF373190, MF373196 and MF373153. CRF85_BC was described by Su et al. 2016, who provided 10 genome sequences (KU992928-KU992937).
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 15YNHS18 (KX582249) B, C X. Xia 4
CRF86_BC was described by Li et al. 2016, who provided 3 genome sequences (KX582249-KX582251).
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 DH32 (KF250408) CRF01, B, C C. Zhang 11
CRF87_cpx was described by Hu et al. 2016, who analyzed previously-published genome sequences and identified 3 having common breakpoints and phylogeny, thus defined as CRF87 (DH32, 09YNLC497, 09YNRL215050).
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 05YNRL25 (KC898979) B, C C. Zhang 3
CRF88_BC was described by Hu et al. 2016, who analyzed previously-published genome sequences and identified 3 having common breakpoints and phylogeny, thus defined as CRF88 (05YNRL25, 05NRL07, DH19).
Breakpoints from Hu et al. 2017.
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
CRF89_BF1 BOL0137 (AY037271) B, F1 M. Thomson 46
CRF89_BF1 was proposed as a new CRF by Michael Thomson, and it seems to be highly related to CRF12_BF. The three sequences initially reported to belong to CRF89_BF1 were KX818199, KX818200 both from Spain, and AY037271 from Bolivia. It was described by Delgado et al. 2021, with additional genome sequences from Spain MW802822-MW802825.
Breakpoints from Michael Thomson, published by Delgado et al. 2021.
1 549 U
550   905   B
906   1184  F1
1185  1340  B
1341  2484  F1
2485  2725  B
2726  2991  F1
2992  3696  B
3697  5942  F1
5943  6173  B
6174  7974  F1
7975  8092  B
8093  8479  F1
8480  8641  B
8642  9470  F1
9471  9719  U
CRF90_BF1 BRGO6043 (KY628221) B, F1 M.N.G. Reis 11
CRF90 was described by Reis et al. 2017, who provided 11 near-full length sequences (KY628215-KY628225). All were from northeastern Brazil with predominantly heterosexual transmission.
Breakpoints from Reis et al. 2017.
626 2661 B
2662 2971 F1
2972 4295 B
4296 4759 F1
4760 8671 B
8672 9492 F1
9493 9612 B
CRF91_cpx () 10

CRF92_C2U DRC699 (MF372647) C, U M. Peeters 11
CRF92 was described by Villbona et al. 2017.
Breakpoints from Villbona et al. 2017.
790 1752 C
1753 2484 U
2485 4274 C
4275 4663 U
4664 8929 C
CRF93_cpx DRC817 (MF372649) A1, A5, C, CRF02, U M. Peeters 3
CRF93 was described by Villbona et al. 2017.
Breakpoints from Villbona et al. 2017.
790 1377 A1
1378 2209 C
2210 2423 U
2424 4303 C
4304 5183 CRF02_AG
5184 5633 A5
5634 8929 CRF02_AG
CRF94_cpx 32FR0916 (MH141494) CRF02, B, F2 M. Wirden 6
CRF94 was described by Mark Wirden et al. 2019 and on poster #958 at the CROI 2018 conference. They identified 6 genome sequences from France (MH141491-MH141494 and MH683549-MH683550). CRF95 was described by Billings et al. 2019. They identified 4 genome sequences from Nigeria (MH666155-MH666158). The prototype sequence is 20428v01 with accession number MH666155.
Breakpoints from Marc Wirden, April 2018.
515    2598  CRF02
2599   4190  B
4191   4919  CRF02
4920   5090  B
5091   5534  F2
5535   9580  B
CRF95_02B 20428v01 (MH666155) CRF02, B E. Billings 12

Breakpoints for CRF95_02B by Brian Foley.
789    1078  CRF02
1079   1189  B
1190   3349  CRF02
3350   3509  B
3510   4008  CRF02
4009   4137  B
4138   4440  CRF02
4441   4796  B
4797   9495  CRF02
CRF96_cpx JL.RF01 (KF850149) CRF01, B, C X. Xia 4
CRF96 was described by Miao et al. 2017.
Breakpoints from Miao et al. 2017.
790 1220 CRF01
1221 1462 B
1463 2604 C
2605 2974 B
2975 4129 CRF01
4130 4359 C
4360 4592 B
4593 4863 C
4864 9348 CRF01
CRF97_01B VI29M2888 (MG760399) CRF01, B 5

CRF98_06B A-Bordeaux (MH479275) CRF06, B P. Recordon-Pinson & H. Fleury 23
CRF98 was described by Recordon-Pinson et al. 2018, working in the lab of Herve Fleury, and the prototype sequence is A-Bordeaux with accession number MH479275.
Breakpoints from Recordon-Pinson et al. 2018.
1 682 U
683 2081  CRF06_cpx 
2082  2181  B
2182  3041  CRF06_cpx
3042  4421  B
4422  4801  CRF06_cpx
4802  5021  B
5022  6281  CRF06_cpx
6282  8361  B
8361  8981  CRF06_cpx
8982  9557  B
9558  9719  U
CRF99_BF1 BRGO4056 (MH986013) B, F1 Monica N. G. Reis 8
CRF99 was described by Reis et al. 2019, who provided 3 near-full length sequences (accession numbers MH986013-MH986015).
Breakpoints from Reis et al. 2019.
1 625 U
626   1378  B
1379  1830  F1
1831  2088  B
2089  2574  F1
2575  5044  B
5045  5944  F1
5945  9489  B
9490  9719  U
CRF100_01C YNLC27 (MH909568) CRF01, C C. Zhang 3
CRF100 was described by Feng et al. 2018, who provided 3 near-full length sequences (accession numbers MH909568-MH909570).
Breakpoints from Feng et al. 2018.
1 680 U
681   3054  CRF01_AE
3055  3355  C
3356  9409  CRF01_AE
9410  9656  C
9656  9719  U
CRF101_01B 07CNYN370 (KF835546) CRF01, B Y. Feng 3
CRF101 was described by Zhang et al. 2019, who provided 2 near-full length sequences (accession numbers MK158945-MK158946) which share the same recombination sites with KF835546.
Breakpoints from Reis et al. 2019.
1 644 U
645   839   CRF01_AE
840   1230  B
1231  3093  CRF01_AE
3094  3188  B
3189  9689  CRF01_AE
9690  9719  U
CRF102_0107 FY058 (MN178644) CRF01, CRF07 X. Li 6
CRF102 was described by Li et al., who provided 2 near-full length sequences (accession numbers MN178644 and MN178645) plus another partial genome MN178645 which shares the same recombination sites.
Breakpoints from jpHMM-HIV.
1 2614 CRF01_AE
2615 3839 CRF07_BC
3840 4170 CRF01_AE
4171 6210 CRF07_BC
6211 6320 CRF01_AE
6321 6490 CRF07_BC
6491 8270 CRF01_AE
8271 8490 CRF07_BC
8491 9719 CRF01_AE
CRF103_01B HE18S0322 (MN067224) CRF01, B 6

Breakpoints from jpHMM-HIV.
789 1050 CRF01_AE
1051 1625 B
1626 2550 CRF01_AE
2551 4400 B
4401 9350 CRF01_AE
9351 9500 B
CRF104_0107 MSM20183420 (MK564326) CRF01, CRF07 M. Zhang 3
CRF104 was described by Chang et al. 2020, who provided 1 near-full length sequence (accession number MK564326) which shares the same recombination sites with MH396608 and MH396609. The first HIV-2 CRF was described by Ibe et al. 2010. They defined the CRF based on 3 recently-isolated genomes from Japan (NMC307, NMC716, NMC842) and 1990 isolate 7312A (L36874) from Cote d'Ivoire.
Breakpoints from Chang et al. 2020.
1 634 U
635  1105  CRF01_AE
1106 3010  CRF07_BC
3011 3727  CRF01_AE
3728 5687  CRF07_BC
5688 9602  CRF01_AE
9603 9719  U
CRF105_0108 LS17S0123 (MN752126) CRF01, CRF08 Y. Shao 5

Breakpoints from Dong et al. 2020.
1 124 U
125 525  CRF01_AE
526  4201  CRF08_BC
4202  9300  CRF01_AE
9302 9719 U
CRF106_cpx LC18S083 (MT276999) CRF01, B, C 10

Breakpoints from Zhou et al. 2020.
1 789 U
790 6039 C
6040 6829 01_AE
6830 8863 C
8864 9026 B
9027 9411 C
9412 9719 U
CRF107_01B HL18S214 (MT712389) CRF01, B 4

Breakpoints from Song et al. 2020.
1 789 U
790 2199 B
2200 2599 CRF01_AE
2600 4999 B
5000 5699 CRF01_AE
5700 9500 B
9501 9719 U
CRF108_BC P4697 (MT559132) B, C 23

Breakpoints from Cañada et al. 2021.
1 570 U
571  4171  C
4172  4467  B
4468  4819  C
4820  5380  B
5381  5564  C
5565  5955  B
5956  8946  C
8947  9386  B
9387  9522  C
9523  9719 U
CRF109_0107 LS11584 (MT919517) CRF01, CRF07 4

Breakpoints from Wang et al. 2020.
1 790 U
791 1170 CRF01_AE
1171  1841  CRF07_BC
1842  2167  CRF01_AE
2168  2463  CRF07_BC
2464  3039  CRF01_AE
3040  3296  CRF07_BC
3297  4239  CRF01_AE
4240  4619  CRF07_BC
4620  5158  CRF01_AE
5159  5887  CRF07_BC
5888  6397  CRF01_AE
6398  8443  CRF07_BC
8444  9412  CRF01_AE
9413  9719  U
CRF110_BC N10189F (MW419275) B, C 3

Breakpoints from Li et al. 2021.
1 790 U
791 3839  C
3840  4135 B
4136  4779  C
4780  5048  B
5049  8759  C
8760  9005  B
9006  9548  C
9549  9719  U
CRF111_01C YN16H12 (MZ327297) CRF01, C 8

Breakpoints from Feng et al. 2021.
1 680 U
681   1527 CRF01_AE
1528  1866 C
1867  3054  CRF01_AE
3055  3355  C
3356  7096  CRF01_AE
7097  7592  C
7593  9409  CRF01_AE
9410  9656  C
9657  9719  U
CRF112_01B 18110456 (MW018130) CRF01, B 4

Breakpoints from Xin et al. 2021.
CRF113_0107 BL3128 (MW018132) CRF01, CRF07 4

CRF114_0155 A18003 (MN654104) CRF01, CRF55 9

CRF115_01C kang019 (KJ778895) CRF01, C Xiaorui Wang 4

CRF116_0108 14YN263 (MT624747) CRF01, CRF08 4

CRF117_0107 17ZJ075 (MK397789) CRF01, CRF07 2

CRF118_BC DH33 (KF250409) B, C 4

Breakpoints from Gao et al. 2021.
1 1234  C
1235  1820 B
1821  2285  C
2286  2840  B
2841  3799  C
3800  4217  B
4218  4540  C
4541  5000  B
5001  6037  C
6038  6200  B
6201  8494  C
8495  8869  B
8870  9719  C
HIV-2 CRFs
HIV2-CRF01_AB 7312A (L36874) HIV2-A, HIV2-B W. Sugiura 73

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

 

last modified: Fri Mar 4 12:38 2022


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