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. We also provide a page listing CRF Breakpoints. If you find any inaccuracies, please contact us.
New CRFs will be numbered sequentially as they become known to us.
Please contact us if you have what you believe to be a new CRF. Because there may be more CRFs about to be published, and because some
authors keep their sequences embargoed until publication, you
must send us: 1) the sequences of the potential new CRF; 2) the subtypes and
breakpoints; and 3) a map of the
subtype mosaic pattern.
If you wish, we will keep this information embargoed until
publication. If your sequences match those 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 |
Author |
| CRF01_AE |
CM240
|
A, E |
J.K. Carr |
| CRF02_AG |
IbNG
|
A, G |
J.K. Carr |
| CRF03_AB |
Kal153
|
A, B |
K. Liitsola |
| CRF04_cpx |
94CY032 |
A, G, H, K, U |
D. Paraskevis |
| CRF05_DF |
VI1310
|
D, F |
T. Laukkanen |
| CRF06_cpx |
BFP90
|
A, G, J, K |
R. B. Oelrichs |
| CRF07_BC |
CN54
|
B', C |
R. Wagner |
| CRF08_BC |
GX-6F
|
B', C |
F.E. McCutchan |
| CRF09_cpx |
96GH2911
|
A, G, U |
F.E. McCutchan |
| CRF10_CD |
TZBF061
|
C, D |
I.N. Koulinska |
| CRF11_cpx |
GR17
|
A, CRF01, G, J |
M. Peeters |
| CRF12_BF |
ARMA159
|
B, F |
J.K. Carr |
| CRF13_cpx |
96CM-1849 |
A, CRF01, G, J, U |
K. Wilbe |
| CRF14_BG |
X397 |
B, G |
R. Najera |
| CRF15_01B |
99TH.MU2079 |
CRF01, B |
F.E. McCutchan |
| CRF16_A2D |
97KR004 |
A2, D |
U. Visawapoka |
| 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 |
CM001BBY |
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 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.
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 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. The recombination breakpoints were discussed in detail by Liitsola et al. 2000.
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 |
The CRF05 chimera was described by Laukkanen et al. 2000. Two genomes (VI1310 and VI961) are 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.
CRF06_cpx |
Reference strain: BFP90 |
Subtypes: A, G, J, K |
Two representatives of this CRF have been fully sequenced: BFP90(AF064699)
from Burkina Faso, described by
Oelrichs et al. 1998, and 95ML84(AJ245481) from Mali, described by
Montavon et al. 1999. The recombinant was previously designated "CRF06_AGJ",
but the subsequent identification of subtype K by Triques et al. 2000 suggested that some regions of CRF06 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 sequenced by Rodenburg et al. 2001 are available:
97CN001 (AF286226)
and 98CN009 (AF286230); however, 97CN001 is reportedly from the same blood sample as CN54.
CRF08_BC |
Reference strain: 97CNGX-6F |
Subtypes: B', C |
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.
CRF09_cpx |
Reference strain: 96GH2911 |
Subtypes: A, G, U |
The CRF09 reference strain was mentioned by McCutchan et al. 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 analyes 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).
CRF10_CD |
Reference strain: TZBF061 |
Subtypes: C, D |
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.
CRF11_cpx |
Reference strain: GR17 |
Subtypes: A, G, CRF01_AE, J |
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.
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:
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: 97KR004 |
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 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.
CRF17_BF |
Reference strain: ARMA038 |
Subtypes: B, F |
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). The structure of ARMA038 was published 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,
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.
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 |
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.
CRF22_01A1 |
Reference strain: CM001BBY |
Subtypes: CRF_01, A1 |
Carr et al. 2001 published an analysis of a novel URF, CM53122, that 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 additional genome sequences, CM3097 and CM001BBY (AY371159). The original CM53122 genome sequence is available in two segments (AY037284 + AY037285). CM001BBY has been chosen here as the reference strain due to the availability of a contiguous full-length sequence. A complete description of this CRF has not yet been published (as of September 2008).
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
reference sequence EE0369 (AY535660) and another CRF06/A1 recombinant 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 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 |
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 Brennan 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.
last modified: Wed Nov 26 14:00 2008
