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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   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
CRF57_BC 1439 B, C L. Li
CRF59_01B 09LNA423 CRF01, B X. Han
CRF61_BC JL100010 B, C X. Li

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
Click to enlargeView breakpoints

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
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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
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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
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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
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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
Click to enlargeView breakpoints

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
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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
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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 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
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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
Click to enlargeView breakpoints

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
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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
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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
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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
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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
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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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
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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
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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
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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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
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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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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).


CRF34_01B

Reference strain: OUR2275P Subtypes: CRF01_AE, B
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
Click to enlargeView breakpoints

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
Click to enlarge View breakpoints

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
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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
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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
Click to enlarge View breakpoints

CRF45 was described by Niama et al. 2009. Genome sequences were identified as 04FR.AKU (EU448295) and 4 additional genomes with accession numbers FN392874-FN392877. 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.


CRF46_BF

Reference strain: 01BR087 Subtypes: B, F1
Click to enlarge View breakpoints

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
Click to enlarge View breakpoints

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
Click to enlarge View breakpoints

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
Click to enlarge View breakpoints

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).


CRF51_01B

Reference sequence: HM021 Subtypes: CRF01_AE, B
Click to enlarge View breakpoints

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
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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
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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
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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
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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.


CRF57_BC

Reference sequence: 1439 Subtypes: B, C
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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. Additional sequences are pending, as of Nov. 2013.


CRF59_01B

Reference sequence: 09LNA423 Subtypes: CRF01_AE, B
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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.


CRF61_BC

Reference sequence: JL100010 Subtypes: B, C
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CRF61 was described by Li et al. 2013. They provided 3 genome sequences from unlinked patients: KC990124, KC990125, KC990126. CRF61 may have originated from two established recombinants, CRF07_BC and CRF08_BC.


HIV-2 CRF


HIV2_CRF01_AB

Reference sequence: 7312A Subtypes: HIV2-A, HIV2-B
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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: Thu Nov 14 10:42 2013


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