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 | A, U | M. Peeters | |
| CRF27 | M. Peeters | ||
| CRF28_BF | BREPM12609 | B, F | R. Diaz |
| CRF29_BF | BREPM16704 | B, F | R. Diaz |
| CRF30_0206 | 00NE36 | 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 | |
| CRF37_cpx | NYU926 | A, G, CRF01, CRF02, U | |
| CRF38 | |||
| CRF39 | |||
| CRF40 | |||
| CRF41 | |||
| CRF42_BF | B, F | J-C. Schmit | |
| CRF43 |
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 submitted to the databases. A patent of the CN54 sequence is available with accession number AX149647 and two other genomes (one, 97CN001 AF286226 is reportedly from the same blood sample as CN54), sequenced by Rodenburg et al. 2001 are available with accession numbers AF286226 and AF286230.
CRF08_BC |
Reference strain: 97CNGX-6F | Subtypes: B', C |
Four near-full-length sequences are available for this CRF: the reference strain and AF286230. 97CNGX-6F, 97CNGX-7F and 97CNGX-9F, all published by Piyasirisilp et al. 2000, and a clone named 98CN006 by Rodenburg et al. 2001. The CRF was first named by F. McCutchan 2000.
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 under accession numbers AY093605 (96GH2911), AY093603 (95SN1795) AY093607 (99DE4057) and AY093604 (95SN7808).
CRF10_CD |
Reference strain: TZBF061 | Subtypes: C, D |
This CRF has been published by Koulinska et al. 2001. Three representatives have been fully sequenced; they are available under accession numbers AF289548, AF289549 and AF289550. It is noteworthy that some regions of these genomes labelled as being derived from 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, one by (Paraskevis et al. 2000) with accession AF179368, and three more by Montavon et al. 2002 accession numbers AJ291718, AJ291719 and AJ291720, and two by Wilbe et al. 2002 accession numbers AF492623 and AF492624.
CRF12_BF |
Reference strain: ARMA159 | Subtypes: B, F |
Four representatives of this CRF, two from Argentina and two from Uruguay, have been fully sequenced and described in an article by Jean Carr et al. 2001. Accession numbers are AY037279, AF385934, AF385935, and AF385936. Two more complete genomes of this CRF, from Argentina, have been described by Thomson et al. 2002. Accession numbers are AF408629 and AF408630. The same group previously sequenced the pol region of B and suspected CRF12_BF isolates in Thomson et al. 2000 accession numbers AF308478 to AF308539. Other BF recombinant sequences sharing some but not all recombination sites with CRF12 are also described in 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 in Wilbe et al. 2002and Kijak et al. 2004. Accession numbers 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 subtype J sequences which are non-recombinant, while the vif, vpr subtype J region is more closely related to non-recombinant J than to CRF11_cpx. More analysis of this CRF has been done and described in Zhang et al. 2005
CRF14_BG |
Reference strain: X397 | Subtypes: B, G |
Six representatives of this CRF, found in Spain, have been sequenced by the group of Rafael Najera (Spain); the sequences have been deposited in GenBank with accession numbers AF423756, AF423757, AF423758, AF423759, AF450096 and AF450097 and are described Delgado et al. 2002.
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. The four sequences have accession numbers 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 |
Two representative complete genomes of this CRF, found in Kenya and South Korea, plus a partial genome 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 from Argentina (ARMA038 AY037281 ARG1139, ARG2233, PSP073, PSP096, BO119 and PCR155) have been sequence, but only ARMA038 has so far (June 2006) 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: AY586545 (Cu103), AY586544 (R77), and DQ020274 (CB134).
CRF21_A2D |
Reference strain: KER2003 | Subtypes: A2, D |
Genome sequences include: AF457051 and AF457072.
CRF22_01A1 |
Reference strain: CM53122 | Subtypes: CRF_01, A1 |
Image Pending.
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 AY900571 (CB118) and AY900572 (CB347).
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 AY900574 (CB378) AY900576 (CB619) AY900575 (CB471), AY900577 (CB228), and AY900581 (CB219).
CRF25_cpx |
CRF26_AU |
CRF27 |
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 |
CRF30 was described by S. Mamadou et al. 2003, but it is not yet clear that 3 complete genomes of the same form have been sequenced yet.
CRF31_BC |
Reference strain: 04BR142 | Subtypes: B, C |
CRF31 was described by Santos et al. 2006. Complete genomes include AY727526, AY727527, and 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: EE0369 (AY535660) and EE0359 (AY535659).
CRF33_01B |
Reference strain: 05MYKL007 | Subtypes: CRF01_AE, B |
CRF33 was described by Tee et al. 2006, who provided 4 genome sequences from Malasia: DQ366659, DQ366660, DQ366661 and 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, OUR2275P, and OUR2478P.
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, AF095, AF104, AF026.
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 and NYU1162. 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 and CM53392. Parts of CRF37 cluster very closely with CRF19.
