title: Identification and genetic characterization of a novel CRF22_01A1 recombinant form of HIV type 1 in Cameroon.
abstract: Cameroon is a country in West Central Africa in which all four groups of HIV-1 (M, N, O, and P), some circulating recombinant forms (CRFs) and unique recombinant forms (URFs) are prevalent. The CRF22 was initially identified through a novel URF strain, 01CM53122, and later defined from two additional sequences; however, the genomic properties of CRF22 have never been demonstrated in detail. In this study, we describe the characterization of five CRF22_01A1 strains, 02CMLT72, 01CM1867LE, 01CM001BBY, 02CM3097MN, and 02CM1917LE, identified in Cameroon without apparent epidemiological links. A typical CRF22_01A1 strain contains five fragments that can be assigned to the CRF01_AE and subsubtype A1 radiations. Forty-eight percent of the genome is classified as CRF01_AE, spanning the entire region of the gag gene, part of the pol gene, and accessory genes as well as the beginning and the end of the env gene and nef gene. Fifty-two percent of the genome is subsubtype A1 including regions mostly in the pol, vif, and env genes. The five CRF22_01A1 viruses formed a deep branch outside the groups of CRF01_AE and displayed similar mosaic structure but were moderately different from the original strain of CRF22_01A1, 01CM53122. Further analysis of the 01CM53122 genome showed that this virus represents a diverse set of mosaic genomes from CRF22_01A1, including a 446-nt segment of 01CM53122 in the env region, but unlike other CRF22 strains, clustered with CRF01_AE rather than the A1 sequence, suggesting that the 01CM53122 strain is a recombinant of CRF22_01A1 and CRF01_AE.
authors.affiliation: Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA.
authors.forename: Jiangqin
authors.initials: J
authors.lastname: Zhao
authors.forename: Shixing
authors.initials: S
authors.lastname: Tang
authors.forename: Viswanath
authors.initials: V
authors.lastname: Ragupathy
authors.forename: Jean K
authors.initials: JK
authors.lastname: Carr
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Wolfe
authors.forename: Bih
authors.initials: B
authors.lastname: Awazi
authors.forename: Indira
authors.initials: I
authors.lastname: Hewlett
mesh_terms: D002163:Cameroon / Q000453:epidemiology; D005814:Genes, Viral; D014644:Genetic Variation; D016679:Genome, Viral; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic; D017423:Sequence Analysis, RNA
chemical_list: D012367:RNA, Viral
references.citation: J Mol Evol. 1995 Mar;40(3):249-59
references.pmid: 7723052
references.citation: AIDS. 1999 Oct 1;13(14):1819-26
references.pmid: 10513639
references.citation: Nature. 1995 Jan 12;373(6510):123-6
references.pmid: 7816094
references.citation: J Virol. 2000 Dec;74(23):11286-95
references.pmid: 11070028
references.citation: J Acquir Immune Defic Syndr. 2007 Jul 1;45(3):361-3
references.pmid: 17592338
references.citation: AIDS Res Hum Retroviruses. 1995 Nov;11(11):1413-6
references.pmid: 8573400
references.citation: Nat Med. 2009 Aug;15(8):871-2
references.pmid: 19648927
references.citation: Virology. 1999 Sep 30;262(2):312-20
references.pmid: 10502510
references.citation: Nature. 2006 Nov 9;444(7116):164
references.pmid: 17093443
references.citation: J Virol. 1999 Jan;73(1):152-60
references.pmid: 9847317
references.citation: AIDS Res Hum Retroviruses. 2004 May;20(5):521-30
references.pmid: 15186527
references.citation: Nature. 1998 Feb 5;391(6667):594-7
references.pmid: 9468138
references.citation: AIDS Res Hum Retroviruses. 2008 Oct;24(10):1309-14
references.pmid: 18851680
references.citation: J Virol. 2000 Nov;74(22):10752-65
references.pmid: 11044120
references.citation: Brief Bioinform. 2008 Jul;9(4):299-306
references.pmid: 18417537
references.citation: J Acquir Immune Defic Syndr. 2008 Dec 1;49(4):432-9
references.pmid: 18931623
references.citation: J Virol. 1996 Oct;70(10):7013-29
references.pmid: 8794346
references.citation: AIDS Res Hum Retroviruses. 2007 Aug;23(8):1008-19
references.pmid: 17725418
references.citation: Science. 1989 Nov 17;246(4932):941-2
references.pmid: 17812579
references.citation: J Infect Dis. 2002 Aug 15;186(4):486-92
references.pmid: 12195375
references.citation: AIDS Res Hum Retroviruses. 2007 Jul;23(7):923-33
references.pmid: 17678477
references.citation: AIDS. 2004 Jul 2;18(10):1478-80
references.pmid: 15199329
references.citation: AIDS. 1994 Oct;8(10):1405-12
references.pmid: 7818811
references.citation: Global Health. 2005 Aug 01;1:13
references.pmid: 16060961
references.citation: AIDS Res Hum Retroviruses. 2004 Dec;20(12):1358-63
references.pmid: 15650429
references.citation: Virology. 2001 Jul 20;286(1):168-81
references.pmid: 11448170
references.citation: J Virol. 2000 Nov;74(22):10498-507
references.pmid: 11044094
references.citation: J Acquir Immune Defic Syndr. 2002 Dec 15;31(5):506-13
references.pmid: 12473839
references.citation: J Acquir Immune Defic Syndr. 1999 Jun 1;21(2):164-71
references.pmid: 10360809
references.citation: J Acquir Immune Defic Syndr Hum Retrovirol. 1999 Apr 15;20(5):481-7
references.pmid: 10225231
references.citation: AIDS Res Hum Retroviruses. 2006 Aug;22(8):812-6
references.pmid: 16910839
references.citation: Science. 2000 Apr 7;288(5463):55-6
references.pmid: 10766634
references.citation: Science. 2006 Jul 28;313(5786):523-6
references.pmid: 16728595
references.citation: J Virol. 1996 Sep;70(9):5935-43
references.pmid: 8709215
references.citation: AIDS Res Hum Retroviruses. 2000 Nov 20;16(17):1831-43
references.pmid: 11118069
references.citation: AIDS. 2001 Oct 19;15(15):F41-7
references.pmid: 11600844
references.citation: Mol Biol Evol. 2007 Aug;24(8):1596-9
references.pmid: 17488738
references.citation: AIDS. 2000;14 Suppl 3:S31-44
references.pmid: 11086847
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W647-51
references.pmid: 19443440
references.citation: J Acquir Immune Defic Syndr. 2006 Jul;42(3):331-41
references.pmid: 16639350
references.citation: AIDS. 2007 Nov;21 Suppl 6:S47-54
references.pmid: 18032938
references.citation: Virology. 1998 Jul 20;247(1):22-31
references.pmid: 9683568