HIV Circulating Recombinant Forms (CRFs)
This page presents an overview of existing circulating recombinant forms
(CRFs). We also provide a page listing CRF Breakpoints.
If you find an inaccuracy, please contact us. For information about subtype and CRF naming, see Nomenclature.
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.
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 |
97CN54
|
B', C |
R. Wagner |
| CRF08_BC |
97CNGX-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, E, G, J, U |
M. Peeters |
| CRF12_BF |
ARMA159
|
B, F1 |
J.K. Carr |
| CRF13_cpx |
96CM-1849 |
CRF01, A, 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, F1 |
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 |
02CMLT72 |
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 |
02CD_MBTB047 |
A, U |
M. Peeters |
| CRF27_cpx |
04FR-KZS |
A, E, G, H, J, K, U |
M. Peeters |
| CRF28_BF |
BREPM12609 |
B, F1 |
R. Diaz |
| CRF29_BF |
BREPM16704 |
B, F1 |
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 |
CRF01, CRF02, A, G |
R. Powell |
| CRF37_cpx |
NYU926 |
CRF01, CRF02, A, G, U |
R. Powell |
| CRF38_BF |
UY03_3389 |
B, F1 |
C. Lopez-Galindez |
| CRF39_BF |
03BRRJ103 |
B, F1 |
M.G. Morgado |
| CRF40_BF |
05BRRJ055 |
B, F1 |
M.G. Morgado |
| CRF41_CD |
CO6650V1 |
C, D |
S. Tovanabutra |
| CRF42_BF |
luBF_13_05 |
B, F1 |
J-C. Schmit |
| CRF43_02G |
J11223 |
CRF02, G |
C. Brennan |
| CRF44_BF |
CH80 |
B, F1 |
M. Thomson |
| CRF45_cpx |
04FR.AKU |
A, K, U |
M. Peeters |
| CRF46_BF |
01BR087 |
B, F1 |
S. S. Sanabani |
| CRF47_BF |
P1942 |
B, F1 |
M. Thomson |
| CRF48_01B |
07MYKT014 |
CRF01, B |
Y. Takebe |
| CRF49_cpx |
N28353 |
A1, C, J, K, U |
T. de Silva & M. Cotten |
| CRF50_A1D |
8179 |
A1, D |
G. Foster |
| CRF51_01B |
HM021 |
CRF01, B |
O.T. Ng |
| CRF52_01B |
M043 |
CRF01, B |
J. Li |
| CRF53_01B |
11FIR164 |
CRF01, B |
K.K. Tee |
| CRF54_01B |
09MYSB023 |
CRF01, B |
K.K. Tee |
| CRF55_01B |
HNCS102056 |
CRF01, B |
X. Han |
| CRF56_cpx |
URF5 |
CRF02, B, G |
M. Leoz |
| CRF57_BC |
1439 |
B, C |
L. Li |
| CRF58_01B |
09MYPR37 |
CRF01, B |
K.K. Tee |
| CRF59_01B |
09LNA423 |
CRF01, B |
X. Han |
| CRF60_BC |
BAV499 |
B, C |
F. Simonetti |
| CRF61_BC |
JL100010 |
B, C |
X. Li |
| CRF62_BC |
YNFL13 |
B, C |
Yiming Shao |
| CRF63_02A1 |
10RU6637 |
CRF02, A1 |
P. Baryshev |
| CRF64_BC |
YNFL31 |
B, C |
Yiming Shao |
| CRF65_cpx |
YNFL05 |
CRF01, B, C |
Yiming Shao |
| CRF66 |
|
|
|
| CRF67_01B |
MAS59 |
CRF01, B |
Jianjun Wu |
| CRF68_01B |
XC46 |
CRF01, B |
Jianjun Wu |
| CRF69_01B |
10JP-5091N200 |
CRF01, B |
J. Hattori |
| CRF70_BF |
PE004 |
B, F1 |
R. Pessoa |
| CRF71_BF |
PE008 |
B, F1 |
R. Pessoa |
| CRF72_BF |
MG002 |
B, F1 |
S. Sanabani |
| CRF73_BG |
9196_01 |
B, G |
M. Thomson |
| CRF74_01B |
10MYPR268 |
CRF01, B |
K.K. Tee |
| CRF75 |
|
|
|
| CRF76_01B |
N628 |
CRF01, B |
A. Hachiya |
| CRF77 |
|
|
|
| CRF78_cpx |
YNTC19 |
CRF01, B, C |
X. Xia |
| CRF79 |
|
|
|
| CRF80 |
|
|
|
| CRF81 |
|
|
|
| CRF82 |
|
|
|
| CRF83 |
|
|
|
| CRF84 |
|
|
|
| CRF85_BC |
SC143 |
B, C |
S. Liang |
| CRF86_BC |
15YNHS18 |
B, C |
X. Xia |
| CRF87_cpx |
DH32 |
CRF01, B, C |
C. Zhang |
| CRF88_BC |
05YNRL25 |
B, C |
C. Zhang |
HIV-2 CRF
| Name |
Reference strain |
Subtypes |
Author |
| HIV2-CRF01_AB |
7312A |
HIV2-A, HIV2-B |
W. Sugiura |
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 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_AB. The use of these parental strains in the analysis revealed an additional segment of subtype A in CRF03_AB (not shown here).
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, 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.
CRF06_cpx |
Reference strain: BFP90 |
Subtypes: A, G, J, K |
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.
CRF07_BC |
Reference strain: 97CN54 |
Subtypes: B', C |
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.
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. Feng et al. 2016 published an analysis of the orgin and breakpoints of CRF07_BC, CRF08_BC, and other BC-derived CRFs.
CRF09_cpx |
Reference strain: 96GH2911 |
Subtypes: A, G, U |
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).
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, E, G, J, U |
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, F1 |
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: CRF01, A, 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 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.
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, F1 |
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).
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: 99KE_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: 02CMLT72 |
Subtypes: CRF01_AE, A1 |
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.
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: 02CM_1918LE |
Subtypes: A, G and U |
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).
CRF26_AU |
Reference strain: 02CD_MBTB047 |
Subtypes: A, U |
CRF26_AU 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 A5. Thus the authors refer to the CRF as CRF26_A5U.
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, F1 |
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, F1 |
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 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).
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: CRF01, CRF02, A, G |
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: CRF01, CRF02, A, G, 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 |
Reference strain: UY03_3389 |
Subtypes: B, F1 |
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.
CRF39_BF |
Reference strain: 03BRRJ103 |
Subtypes: B, F1 |
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, F1 |
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: J11223 |
Subtypes: CRF02_AG, G |
Yamaguchi et al. 2008 described 4 complete genomes from Saudi Arabia: J11223 (EU697904), J11232 (EU697905), J11243 (EU697907), and J11456 (EU697909).
CRF44_BF |
Reference strain: CH80 |
Subtypes: B, F1 |
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.
CRF45_cpx |
Reference strain: 04FR.AKU |
Subtypes: A, K, U |
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.
CRF46_BF |
Reference strain: 01BR087 |
Subtypes: B, F1 |
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.
CRF47_BF |
Reference strain: P1942 |
Subtypes: B, F1 |
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.
CRF48_01B |
Reference sequence: 07MYKT014 |
Subtypes: CRF01, B |
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.
CRF49_cpx |
Reference sequence: N28353 |
Subtypes: A1, C, J, K, U |
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).
CRF50_A1D |
Reference sequence: 8179 |
Subtypes: A1, D |
CRF51 was described by Foster et al. 2014. They provided 5 genome sequences from MSM in the UK (JN417236, JN417237, JN417239, JN417240, JN417241).
CRF51_01B |
Reference sequence: HM021 |
Subtypes: CRF01_AE, B |
CRF51 was described by Ng et al. 2011. They provided 3 genome
sequences from patients in Singapore: HM021, HM062, and HM091 (JN029801-JN029803).
CRF52_01B |
Reference sequence: M043 |
Subtypes: CRF01_AE, B |
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).
CRF53_01B |
Reference sequence: 11FIR164 |
Subtypes: CRF01_AE, B |
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.
CRF54_01B |
Reference sequence: 09MYSB023 |
Subtypes: CRF01_AE, B |
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.
CRF55_01B |
Reference sequence: HNCS102056 |
Subtypes: CRF01_AE, B |
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.
CRF56_cpx |
Reference sequence: URF5 |
Subtypes: CRF02, B, G |
CRF56 was described by Leoz et al. 2013. They presented 4 genome sequences from unlinked MSM in Paris, France.
CRF57_BC |
Reference sequence: 1439 |
Subtypes: B, C |
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).
CRF58_01B |
Reference sequence: 09MYPR37 |
Subtypes: CRF01_AE, B |
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.
CRF59_01B |
Reference sequence: 09LNA423 |
Subtypes: CRF01_AE, B |
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.
CRF60_BC |
Reference sequence: BAV499 |
Subtypes: B, C |
CRF60 was described by Simonetti et al. 2013. They provided 3 genome sequences from unlinked patients from Italy: KC899079-KC899081.
CRF61_BC |
Reference sequence: JL100010 |
Subtypes: B, C |
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.
CRF62_BC |
Reference sequence: YNFL13 |
Subtypes: B, C |
CRF62 was described by Wei et al. 2014b. They provided 3 genome sequences from unlinked patients in Dehong Prefecture, Yunnan, China (KC870034, KC870035, KC870037).
CRF63_02A1 |
Reference sequence: 10RU6637 |
Subtypes: CRF02, A1 |
CRF63 was described by Baryshev et al. 2014, who identified 8 genome sequences from Russia (JN230353, JX500698-JX500705).
CRF64_BC |
Reference sequence: YNFL31 |
Subtypes: B, C |
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.
CRF65_cpx |
Reference sequence: YNFL05 |
Subtypes: CRF01, B, C |
CRF65 was described by Feng et al. 2014, who provided 4 genome sequences (KC183778, KC870027, KC870028, KC870030).
CRF67_01B |
Reference sequence: MAS59 |
Subtypes: CRF01, B |
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).
CRF68_01B |
Reference sequence: XC46 |
Subtypes: CRF01, B |
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.
CRF69_01B |
Reference sequence: 10JP-5091N200 |
Subtypes: CRF01, B |
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.
CRF70_BF |
Reference sequence: PE004 |
Subtypes: B, F1 |
Pessoa et al. 2014b identified CRF70 and CRF71 among blood donors in Pernambuco, Brazil. CRF70 was documented with 4 near-full-length genomes.
CRF71_BF |
Reference sequence: PE008 |
Subtypes: B, F1 |
Pessoa et al. 2014b identified CRF70 and CRF71 among blood donors in Pernambuco, Brazil. CRF71 was documented with 12 near-full-length genomes.
CRF72_BF |
Reference sequence: MG002 |
Subtypes: B, F1 |
CRF72 was described by Pessoa et al. 2014a, who provided 5 genome sequences (KJ671533-KJ671537).
CRF73_BG |
Reference sequence: 9196_01 |
Subtypes: B, G |
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.
CRF74_01B |
Reference sequence: 10MYPR268 |
Subtypes: CRF01, B |
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.
CRF76_01B |
Reference sequence: N628 |
Subtypes: CRF01, B |
CRF76 was described by Ogawa et al. 2016, who provided 3 genome sequences from Japan.
CRF78_cpx |
Reference sequence: YNTC19 |
Subtypes: CRF01, B, C |
CRF78 was described by Song et al. 2016, who provided 3 genome sequences from Yunnan, China (KU161143-KU161145).
CRF85_BC |
Reference sequence: SC143 |
Subtypes: B, C |
CRF85_BC was described by Su et al. 2016, who provided 10 genome sequences (KU992928-KU992937).
CRF86_BC |
Reference sequence: 15YNHS18 |
Subtypes: B, C |
CRF86_BC was described by Li et al. 2016, who provided 3 genome sequences (KX582249-KX582251).
CRF87_cpx |
Reference sequence: 15YNHS18 |
Subtypes: CRF01, B, C |
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).
CRF88_BC |
Reference sequence: 05YNRL25 |
Subtypes: B, C |
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).
HIV-2 CRF
HIV2_CRF01_AB |
Reference sequence: 7312A |
Subtypes: HIV2-A, HIV2-B |
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.
last modified: Tue Jan 3 12:32 2017
