The Circulating Recombinant Forms (CRFs)
On this page we present an overview of existing circulating recombinant forms (CRFs) and announce new ones as they are described. You can check here to find out if your new sequence conforms with the mosaic pattern of any existing CRF. If not, please contact us to assign a new CRF number. New CRFs will be numbered sequentially as they become known to us. Because there may be more CRFs about to be published, and because some authors want to keep their sequences embargoed until publication, you must send us: 1) the potentially new CRF sequences; 2) the subtypes and breakpoints; and 3) a map of the subtype mosaic pattern. To avoid confusion from double designations etc, we will then compare that information to what is available to us. If you wish, we will keep also your sequences embargoed until publication. If your sequences match that of some other embargoed sequences, we may put you in contact with the other authors so you can discuss your findings.
The Recombinant HIV-1 Drawing tool provides a handy way to produce a quality drawing of your CRFs and URFs.
| Name | Reference strain | Subtypes | Corresponding author |
|---|---|---|---|
| CRF01_AE | CM240 | A, E | Listed below |
| CRF02_AG | IbNG | A, G | Listed below |
| CRF03_AB | Kal153 | A, B | Listed below |
| CRF04_cpx | 94CY032 | A, G, H, K, U | Listed below |
| CRF05_DF | VI1310 | D, F | Listed below |
| CRF06_cpx | BFP90 | A, G, J, K | Listed below |
| CRF07_BC | CN54 | B', C | Listed below |
| CRF08_BC | GX-6F | B', C | Listed below |
| CRF09_cpx | 96GH2911 | CRF02, A, U | Listed below |
| CRF10_CD | TZBF061 | C, D | Listed below |
| CRF11_cpx | GR17 | A, CRF01, G, J | Listed below |
| CRF12_BF | ARMA159 | B, F | Listed below |
| CRF13_cpx | 96CM-1849 | A, CRF01, G, J, U | Listed below |
| CRF14_BG | X397 | B, G | Listed below |
| CRF15_01B | 99TH.MU2079 | CRF01, B | Listed below |
| CRF16_A2D | KISII5009 | A2, D | Listed below |
| CRF17_BF | ARMA038 | B, F | J.K. Carr |
| CRF18_cpx | CU76 | A1, F, G, H, K, U | M. Thomson |
| CRF19_cpx | CU7 | A1, D, G | M. Thomson |
| CRF20_BG | Cu103 | B, G | M. Thomson |
| CRF21_A2D | 99KE_KER2003 | A2, D | F.E. McCutchan |
| CRF22_01A1 | CM53122 | CRF01, A1 | J.K. Carr |
| CRF23_BG | CB118 | B, G | M. Thomson |
| CRF24_BG | CB378 | B, G | M. Thomson |
| CRF25_cpx | 02CM_1918LE | A, G, U | J.K. Carr |
| CRF26_AU | MBTB047 | A, U | M. Peeters |
| CRF27_cpx | 04FR-KZS | A, E, G, H, J, K, U | M. Peeters |
| CRF28_BF | BREPM12609 | B, F | R. Diaz |
| CRF29_BF | BREPM16704 | B, F | R. Diaz |
| CRF30_0206 | NE36 | CRF02, CRF06 | M. Peeters |
| CRF31_BC | 04BR142 | B, C | M. Soares |
| CRF32_06A1 | EE0369 | CRF06, A1 | M. Adojaan |
| CRF33_01B | 05MYKL007 | CRF01, B | K.P. Ng & K.K. Tee |
| CRF34_01B | OUR2275P | CRF01, B | F.E. McCutchan |
| CRF35_AD | AF095 | A, D | F.E. McCutchan |
| CRF36_cpx | NYU830 | A, G, CRF01, CRF02 | R. Powell |
| CRF37_cpx | NYU926 | A, G, CRF01, CRF02, U | R. Powell |
| CRF38_BF | GDJE | B, F | C. Lopez-Galindez |
| CRF39_BF | 03BRRJ103 | B, F | M.G. Morgado |
| CRF40_BF | 05BRRJ055 | B, F | M.G. Morgado |
| CRF41_CD | CO6650V1 | C, D | S. Tovanabutra |
| CRF42_BF | luBF_13_05 | B, F1 | J-C. Schmit |
| CRF43 | CRF02, G | C. Brennan |
CRF01_AE |
Reference strain: CM240 | Subtypes: A, E |
CRF01_AE (reference strain CM240) represents a putative subtype A/E recombinant form of HIV-1 which is spreading epidemically in Asia, but originated from Central Africa (Murphy et al. 1993; Carr et al. 1996; Gao et al. 1996). In the future, putative recombinants with only one full-length "parental" subtype representative would be designated as being comprised of this subtype and unclassified regions (U). Under the new nomenclature system CRF01_AE would be referred to as CRF01_AU because the putative "parental" non-recombinant E strain has not been found. But, as the "E" designation for the env region of these strains is very commonly used, renaming it would lead to confusion. Thus, the "E" designation will be retained.
CRF02_AG |
Reference strain:IbNG | Subtypes: A, G |
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).
CRF03_AB |
Reference strain:Kal153 | Subtypes: A, B |
CRF03_AB represents a subtype A/B recombinant form that was first found in Kaliningrad, and is circulating in Russian and Ukrainian cities, primarily in injecting drug users (Liitsola et al. 1998; Lukashov 1999). Circulation of this strain appears to have been accelerated by intravenous injection of a locally produced opiate contaminated with HIV infected blood.
CRF04_cpx |
Reference strain:94CY032 | Subtypes: A, G, H, K, U |
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.
CRF05_DF |
Reference strain: VI1310 | Subtypes: D, F |
Presently, two complete genomes (VI1310 and VI961), both strains from Belgian individuals presumably infected by partners for the Democratic Republic of the Congo (DRC), former Zaire) and some fragments are available of this mosaic, so formally it does not yet qualify as a CRF. The chimera is described by Laukkanen et al. 2000.
CRF06_cpx |
Reference strain:BFP90 | Subtypes: A, G, J, K |
Two representatives of this CRF have been fully sequenced, BFP90 from Burkina Faso, described in Oelrichs et al. 1998, and 95ML84, from Mali, published by Montavon et al. 1999. The recombinant was previously designated "CRF06_AGJ", but recent results from Triques et al. 2000 suggest that the unidentified regions are subtype K, so the subtype is now called "CRF06_cpx".
CRF07_BC |
Reference strain: 97CN54 | Subtypes: B', C |
A description of this CRF was published by Su, L. 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 (one, 97CN001, is reportedly from the same blood sample as CN54), sequenced by Rodenburg et al. 2001 are available: 97CN001 (AF286226) and 98CN009 (AF286230).
CRF08_BC |
Reference strain: 97CNGX-6F | Subtypes: B', C |
The CRF was first named by F. McCutchan 2000. Four near-full-length sequences are available for this CRF: 97CNGX-6F (AY008715), 97CNGX-7F (AY008716) and 97CNGX-9F (AY008717), all published by Piyasirisilp et al. 2000, and a clone named 98CN006 (AF286229) by Rodenburg et al. 2001.
CRF09_cpx |
Reference strain: P2911 | Subtypes: CRF02_AG, A, U |
The CRF and reference strain were mentioned in F. McCutchan 2000, and Brodine 2003. The full mosaic structure was mapped in McCutchan 2004. Sequences of four complete genomes are available: 96GH2911 (AY093605), 95SN1795 (AY093603), 99DE4057 (AY093607), and 95SN7808 (AY093604).
CRF10_CD |
Reference strain: TZBF061 | Subtypes: C, D |
This CRF was published by Koulinska et al. 2001. Three representatives have been fully sequenced: 81200">TZBF061 (AF289548), 81199">TZBF071 (AF289549) and 81198">TZBF110 (AF289550). It is noteworthy that some regions of these genomes labelled as subtype D are nearly equidistant between subtypes B and D.
CRF11_cpx |
Reference strain: GR17 | Subtypes: A, G, CRF01_AE, J |
Six representatives of this CRF has been fully sequenced and released to the public: 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 .
CRF12_BF |
Reference strain: ARMA159 | Subtypes: B, F |
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.
CRF13_cpx |
Reference strain: 96CM-1849 | Subtypes: A, CRF01_AE, CRF11_cpx, G, J, U |
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 rlated 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
CRF14_BG |
Reference strain: X397 | Subtypes: B, G |
Six representatives of this CRF, found in Spain, were sequenced by the group of Rafael Najera and described by Delgado et al. 2002: 105642">AF423756, AF423757, AF423758, AF423759, AF450096, and AF450097.
CRF15_01B |
Reference strain: 99TH.MU2079 | Subtypes: CRF01_AE, B |
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.
CRF16_A2D |
Reference strain: 00KE_KISII5009 | Subtypes: A2, D |
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 with accession numbers AF457060 and AF286239 are the complete genomes. Note that AF457060 is hypermutated.
CRF17_BF |
Reference strain: ARMA038 | Subtypes: B, F |
Image Pending.
This CRF shares some breakpoints with CRF12_BF. Several genomes of CRF17 have been sequenced: ARMA038 (AY037281), ARG1139 (EU581825), ARG2233 (EU581826), PSP073 (EU581824), PSP096 (EU581823), BO119 (EU581827), and PCR155 (EU581828). Only ARMA038 has so far (August 2008) been published in an article by Carr et al. 2001.
CRF18_cpx |
Reference strain: CU76 | Subtypes: A1, F, G, H, K, U |
CRF18 was described by Thomson et al. 2005 , who provided two genome sequences, AY586540 and AY586541.
CRF19_cpx |
Reference strain: CU7 | Subtypes: A1, D, G |
CRF19 was described by Casado et al. 2005, who provided three genome sequences, AY894994, AY588970, and AY588971.
CRF20_BG |
Reference strain: Cu103 | Subtypes: B, G |
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).
CRF21_A2D |
Reference strain: KER2003 | Subtypes: A2, D |
Genome sequences include: AF457051 and AF457072.
CRF22_01A1 |
Reference strain: CM53122 | Subtypes: CRF_01, A1 |
Genome sequences include: AY037284 and AY371159.
CRF23_BG |
Reference strain: CB118 | Subtypes: B, G |
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).
CRF24_BG |
Reference strain: CB378 | Subtypes: B, G |
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).
CRF25_cpx |
Reference strain: 01CM.101BA | Subtypes: A, G and U |
CRF25_cpx is described by two complete genomes and other data by J. Carr. The two genomes are named 01CM.101BA DQ826726 and 02CM.2931HA AY371169.
CRF26_AU |
Reference strain: 02CD_MBTB047 | Subtypes: A, U |
CRF26_AU is described by four complete genomes by M. Peeters. The names of the genomes are 02CD_KS069, 97CD_KTB119, 02CD_LBT084 and 02CD_MBTB047
CRF27_cpx |
Reference strain: 04FR-KZS | Subtypes: A, E, G, H, J, K, U |
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).
CRF28_BF |
Reference strain: BREPM12609 | Subtypes: B, F |
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.
CRF29_BF |
Reference strain: BREPM16704 | Subtypes: B, F |
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.
CRF30_0206 |
Reference strain: 00NE36 | Subtypes: CRF02_AG, CRF06_cpx |
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.
CRF31_BC |
Reference strain: 04BR142 | Subtypes: B, C |
CRF31 was described by Santos et al. 2006. Complete genomes include 04BR137 AY727526, 04BR142 AY727527, and 110PA EF091932, all from Brazil.
CRF32_06A1 |
Reference strain: EE0369 | Subtypes: CRF06_cpx, A1 |
CRF32 was described by Adojaan et al. 2005, who provided 2 genome sequences: EE0359 AY535659 and EE0369 AY535660. However, EE0359 AY535659 is CRF06_cpx across the entire genome, and not recombinant with subtype A1. The other CRF06/A1 recombinant is EST2002_1169 DQ167215.
CRF33_01B |
Reference strain: 05MYKL007 | Subtypes: CRF01_AE, B |
CRF33 was described by Tee et al. 2006, who provided 4 genome sequences from Malasia: 05MYKL007_1 DQ366659, 05MYKL015_2 DQ366660, 05MYKL031_1 DQ366661 and 05MYKL045_1 DQ366662.
CRF34_01B |
Reference strain: OUR2275P | Subtypes: CRF01_AE, B |
CRF34 was described by Tovanabutra et al. 2007 based on 3 genome sequences from Thailand: OUR1969P EF165539, OUR2275P EF165540, and OUR2478P EF165541.
CRF35_AD |
Reference strain: AF095 | Subtypes: A, D |
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.
CRF36_cpx |
Reference strain: NYU830 | Subtypes: A, G, CRF01, CRF02 |
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.
CRF37_cpx |
Reference strain: NYU926 | Subtypes: A, G, CRF01, CRF02, U |
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.
CRF38_BF |
CRF38 has not yet been published (August 2008), but 3 genomes from Uruguay have been sequenced: GDJE, NSDA and GH. These sequences have been submitted to GenBank and are available from Dr Cecilio Lopez-Galindez upon request.
CRF39_BF |
Reference strain: 03BRRJ103 | Subtypes: B, F |
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.
CRF40_BF |
Reference strain: 05BRRJ055 | Subtypes: B, F |
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.
CRF41_CD |
Reference strain: CO6650V1 | Subtypes: C, D |
CRF41_CD has not yet been published (August 2008) but it is based on 3 genomes by Sodsai Tovanabutra: CO6650V1, CO6952V1, and CO6577V5.
CRF42_BF |
Reference strain: luBF_13_05 EU170136 | Subtypes: B, F1 |
CRF42_BF is described by D. Struck et al. in press (August 2008). There were 21 complete genomes sequenced, with accession numbers EU170135..EU170155.
CRF43_02G |
Reference strain: Not yet specified | Subtypes: CRF02_AG, G |
Catherine Brennen described 4 complete genomes at the Conference on Retroviruses and Opportunistic Infections, February 2008. The names of the genomes are J11223, J11232, J11243 and J11456.