title: Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions.
authors.forename: Bluma
authors.initials: B
authors.lastname: Brenner
authors.forename: Mark A
authors.initials: MA
authors.lastname: Wainberg
authors.forename: Michel
authors.initials: M
authors.lastname: Roger
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000517:prevention & control / Q000635:transmission; D000890:Anti-Infective Agents; D023241:Antiretroviral Therapy, Highly Active; D016000:Cluster Analysis; D024921:Drug Resistance, Multiple, Viral / Q000235:genetics; D058872:Epidemics; D019143:Evolution, Molecular; D005260:Female; D015658:HIV Infections / Q000235:genetics / Q000517:prevention & control* / Q000635:transmission*; D015497:HIV-1 / Q000235:genetics; D006297:Health Services Accessibility / Q000706:statistics & numerical data*; D006801:Humans; D018445:Infectious Disease Transmission, Vertical / Q000517:prevention & control* / Q000706:statistics & numerical data; D008297:Male; D010802:Phylogeny; D060386:Sex Workers; D012725:Sexual Behavior / Q000706:statistics & numerical data*; D014171:Transients and Migrants; D016903:Drug Monitoring
chemical_list: D000890:Anti-Infective Agents
references.citation: Expert Opin Biol Ther. 2002 Oct;2(7):751-61
references.pmid: 12387674
references.citation: N Engl J Med. 2012 Aug 2;367(5):423-34
references.pmid: 22784038
references.citation: AIDS. 2010 Jan 16;24(2):271-82
references.pmid: 20010072
references.citation: Clin Infect Dis. 2010 May 15;50 Suppl 3:S102-7
references.pmid: 20397937
references.citation: AIDS. 2005 Mar 4;19(4):449-50
references.pmid: 15750402
references.citation: PLoS One. 2011 Mar 02;6(3):e16986
references.pmid: 21399681
references.citation: J Infect Dis. 2010 May 15;201(10):1488-97
references.pmid: 20384495
references.citation: J Infect Dis. 2011 Oct 1;204(7):1115-9
references.pmid: 21881127
references.citation: PLoS One. 2010 Apr 12;5(4):e10148
references.pmid: 20405044
references.citation: PLoS One. 2012;7(10):e47289
references.pmid: 23056619
references.citation: AIDS. 2011 Feb 20;25(4):473-7
references.pmid: 21160416
references.citation: Curr Opin Infect Dis. 2006 Dec;19(6):594-606
references.pmid: 17075337
references.citation: AIDS. 2005 Oct 14;19(15):1555-64
references.pmid: 16184024
references.citation: AIDS. 2009 Jul 17;23(11):1415-23
references.pmid: 19487906
references.citation: J Acquir Immune Defic Syndr. 2013 Jan 1;62(1):102-8
references.pmid: 23075917
references.citation: Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7427-31
references.pmid: 8755490
references.citation: J Infect Dis. 2012 Feb 1;205(3):351-2
references.pmid: 22241799
references.citation: BMC Infect Dis. 2010 Sep 07;10:262
references.pmid: 20822507
references.citation: AIDS. 2007 Aug 20;21(13):1723-30
references.pmid: 17690570
references.citation: J Infect Dis. 2009 Nov 15;200(10):1503-8
references.pmid: 19835478
references.citation: AIDS. 2011 Jul 17;25(11):1371-7
references.pmid: 21522007
references.citation: J Infect Dis. 2005 May 1;191(9):1403-9
references.pmid: 15809897
references.citation: J Infect Dis. 2012 Feb 15;205(4):521-4
references.pmid: 22207652
references.citation: Mol Phylogenet Evol. 2012 Feb;62(2):777-92
references.pmid: 22138161
references.citation: PLoS Med. 2012;9(7):e1001239
references.pmid: 22802729
references.citation: PLoS One. 2010 Jun 10;5(6):e11068
references.pmid: 20548786
references.citation: J Infect Dis. 2010 Jun 1;201(11):1697-702
references.pmid: 20423223
references.citation: AIDS Rev. 2012 Apr-Jun;14(2):83-100
references.pmid: 22627605
references.citation: J Virol. 1993 Jan;67(1):222-8
references.pmid: 8380072
references.citation: Microbiol Mol Biol Rev. 2009 Sep;73(3):451-80, Table of Contents
references.pmid: 19721086
references.citation: Lancet. 2011 Jul 16;378(9787):256-68
references.pmid: 21684591
references.citation: J Virol. 2010 Jun;84(12):6241-7
references.pmid: 20375173
references.citation: J Virol. 2012 Jun;86(12):6835-46
references.pmid: 22514337
references.citation: Epidemiology. 2010 Sep;21(5):669-75
references.pmid: 20585251
references.citation: PLoS Pathog. 2012;8(5):e1002686
references.pmid: 22693444
references.citation: AIDS Res Hum Retroviruses. 2012 Oct;28(10):1280-4
references.pmid: 22364163
references.citation: N Engl J Med. 2012 Aug 2;367(5):411-22
references.pmid: 22784040
references.citation: N Engl J Med. 2011 Aug 18;365(7):637-46
references.pmid: 21848464
references.citation: Lancet. 2010 Aug 14;376(9740):532-9
references.pmid: 20638713
references.citation: PLoS Pathog. 2011 Feb 10;7(2):e1001273
references.pmid: 21347345
references.citation: N Engl J Med. 2010 Dec 30;363(27):2587-99
references.pmid: 21091279
references.citation: J Infect Dis. 2007 Apr 1;195(7):924-6
references.pmid: 17330780
references.citation: AIDS Rev. 2003 Jan-Mar;5(1):52-61
references.pmid: 12875108
references.citation: Curr Opin HIV AIDS. 2010 Jul;5(4):283-90
references.pmid: 20543602
references.citation: Lancet. 2012 Jul 28;380(9839):424-38
references.pmid: 22819663
references.citation: Int J STD AIDS. 2004 Oct;15(10):691-6
references.pmid: 15479507
references.citation: PLoS Pathog. 2009 Sep;5(9):e1000590
references.pmid: 19779560
references.citation: Can J Public Health. 2011 Mar-Apr;102(2):90-6
references.pmid: 21608378
references.citation: Curr Opin HIV AIDS. 2012 Mar;7(2):117-24
references.pmid: 22258501
references.citation: AIDS. 2010 Aug 24;24(13):2081-8
references.pmid: 20671545
references.citation: AIDS. 2011 May 15;25(8):1103-12
references.pmid: 21505305
references.citation: Lancet Infect Dis. 2011 May;11(5):363-71
references.pmid: 21354861
references.citation: AIDS Res Hum Retroviruses. 2013 Feb;29(2):329-36
references.pmid: 22906365
references.citation: Antivir Ther. 2011;16(8):1347-50
references.pmid: 22155917
references.citation: Euro Surveill. 2011 Sep 08;16(36):
references.pmid: 21924120
references.citation: PLoS One. 2012;7(6):e39819
references.pmid: 22768132
references.citation: Lancet. 2010 Jun 12;375(9731):2092-8
references.pmid: 20537376
references.citation: HIV Ther. 2009 Nov 1;3(6):583-594
references.pmid: 20190870
references.citation: Clin Infect Dis. 2011 Feb 15;52(4):532-9
references.pmid: 21220770
references.citation: AIDS. 2004 Apr 9;18(6):909-15
references.pmid: 15060438
references.citation: J Infect Dis. 2007 Apr 1;195(7):951-9
references.pmid: 17330784
references.citation: AIDS Res Hum Retroviruses. 2012 Aug;28(8):928-32
references.pmid: 22049908
references.citation: J Acquir Immune Defic Syndr. 2010 Sep;55(1):102-8
references.pmid: 20622676
references.citation: AIDS. 2010 Jul 17;24(11):1739-47
references.pmid: 20588173
references.citation: AIDS Res Hum Retroviruses. 2010 Nov;26(11):1233-8
references.pmid: 20860534
references.citation: J Virol. 2008 Apr;82(8):3952-70
references.pmid: 18256145
references.citation: PLoS One. 2012;7(6):e39872
references.pmid: 22768150
references.citation: Retrovirology. 2009 May 20;6:49
references.pmid: 19457244
references.citation: PLoS One. 2009;4(3):e4724
references.pmid: 19266092
references.citation: J Virol. 2009 Mar;83(6):2715-27
references.pmid: 19116249
references.citation: J Infect Dis. 2012 Feb 15;205(4):528-34
references.pmid: 22207651
references.citation: AIDS. 2007 Oct 18;21(16):2223-9
references.pmid: 18090050
references.citation: J Infect Dis. 2011 Dec 15;204(12):1918-26
references.pmid: 21990420
references.citation: J Infect Dis. 2011 Oct 1;204(7):1095-103
references.pmid: 21881125
references.citation: J Clin Microbiol. 2012 Feb;50(2):407-13
references.pmid: 22162552
references.citation: Retrovirology. 2010 Mar 23;7:25
references.pmid: 20331894
references.citation: PLoS Comput Biol. 2012;8(6):e1002552
references.pmid: 22761556
references.citation: Sex Transm Dis. 2008 Jan;35(1):25-9
references.pmid: 17898678
references.citation: AIDS. 2004 Mar 26;18(5):719-28
references.pmid: 15075506
references.citation: Science. 2004 Jan 16;303(5656):327-32
references.pmid: 14726583
references.citation: AIDS Rev. 2012 Apr-Jun;14(2):154
references.pmid: 22792582
references.citation: J Virol. 2011 Oct;85(20):10755-63
references.pmid: 21795343
references.citation: Curr Opin HIV AIDS. 2010 Jul;5(4):265-8
references.pmid: 20539086
references.citation: AIDS. 2012 Oct 23;26(16):2079-86
references.pmid: 23052354
references.citation: J Acquir Immune Defic Syndr. 2012 Sep 1;61(1):1-8
references.pmid: 22592583
references.citation: J Infect Dis. 2010 Apr 15;201 Suppl 1:S7-15
references.pmid: 20225950
references.citation: Sex Transm Infect. 2011 Jun;87(4):289-91
references.pmid: 21441275
references.citation: Med Microbiol Immunol. 2012 Aug;201(3):259-69
references.pmid: 22262052
references.citation: Clin Infect Dis. 2011 Jun;52(11):1363-70
references.pmid: 21596678
references.citation: J Infect Dis. 2008 Sep 1;198(5):687-93
references.pmid: 18662132
references.citation: Clin Infect Dis. 2012 Oct;55(8):1135-43
references.pmid: 22784872
references.citation: AIDS. 2008 May 31;22(9):1071-7
references.pmid: 18520351
references.citation: AIDS. 2006 Jun 12;20(9):F9-13
references.pmid: 16816549
references.citation: Am J Public Health. 2012 May;102 Suppl 2:S242-9
references.pmid: 22401516
references.citation: Epidemiology. 2010 Sep;21(5):676-84
references.pmid: 20571409
references.citation: J Acquir Immune Defic Syndr. 2008 Oct 1;49(2):205-11
references.pmid: 18769347
references.citation: JAMA. 2012 Jul 25;308(4):387-402
references.pmid: 22820792
references.citation: AIDS. 2011 Mar 13;25(5):679-89
references.pmid: 21297424
references.citation: AIDS. 2006 Jun 26;20(10):1447-50
references.pmid: 16791020
references.citation: J Virol. 2002 Feb;76(4):1753-61
references.pmid: 11799170
references.citation: AIDS Res Hum Retroviruses. 2012 Aug;28(8):885-93
references.pmid: 22206228
references.citation: N Engl J Med. 2011 Aug 11;365(6):493-505
references.pmid: 21767103
references.citation: Sci China Life Sci. 2012 Apr;55(4):328-35
references.pmid: 22566089
references.citation: Sex Transm Infect. 2007 Aug;83(5):387-91
references.pmid: 17314129
references.citation: AIDS. 2011 Nov 13;25(17):2157-65
references.pmid: 21866038
references.citation: AIDS Care. 2012;24(11):1416-24
references.pmid: 22292863
references.citation: Science. 2000 Jun 9;288(5472):1789-96
references.pmid: 10846155
references.citation: MMWR Suppl. 2012 Jun 15;61(2):57-64
references.pmid: 22695465
references.citation: Crit Rev Clin Lab Sci. 2010 Jan-Feb;47(1):5-49
references.pmid: 20367503
references.citation: PLoS One. 2010 Dec 10;5(12):e15510
references.pmid: 21170322
references.citation: J Virol. 2002 Jan;76(1):397-405
references.pmid: 11739704
references.citation: Curr Opin HIV AIDS. 2011 Jul;6(4):315-25
references.pmid: 21646878
references.citation: AIDS. 2005 Jan 3;19(1):85-90
references.pmid: 15627037
references.citation: PLoS One. 2011;6(6):e21241
references.pmid: 21698125
references.citation: Epidemics. 2010 Sep;2(3):155-164
references.pmid: 21352786
references.citation: BMC Bioinformatics. 2010 Oct 25;11:532
references.pmid: 20973976
references.citation: MMWR Morb Mortal Wkly Rep. 2005 Jun 24;54(24):597-601
references.pmid: 15973239
references.citation: MMWR Morb Mortal Wkly Rep. 2012 Jun 22;61(24):441-5
references.pmid: 22717512
references.citation: AIDS. 2001 Nov 23;15(17):2287-92
references.pmid: 11698702
references.citation: J Clin Microbiol. 2012 Sep;50(9):3054-9
references.pmid: 22785188
references.citation: Trends Microbiol. 1996 Jan;4(1):16-21
references.pmid: 8824790
references.citation: PLoS Pathog. 2009 May;5(5):e1000414
references.pmid: 19424423
references.citation: AIDS. 2011 Jul 31;25(12):1515-22
references.pmid: 21505307
references.citation: Epidemics. 2009 Dec;1(4):230-9
references.pmid: 21352769
references.citation: J Virol. 2008 Dec;82(23):11609-18
references.pmid: 18786994
references.citation: Infect Genet Evol. 2012 Jul;12(5):1052-7
references.pmid: 22430050
references.citation: J Acquir Immune Defic Syndr (1988). 1994 Nov;7(11):1169-84
references.pmid: 7932084
references.citation: J Virol. 2009 Mar;83(6):2645-54
references.pmid: 19158238
references.citation: PLoS One. 2011 Feb 09;6(2):e16714
references.pmid: 21415914
references.citation: AIDS. 2010 Mar 27;24(6):907-13
references.pmid: 20139750
references.citation: PLoS Pathog. 2009 Jan;5(1):e1000274
references.pmid: 19165325
references.citation: PLoS One. 2011 Jan 31;6(1):e16551
references.pmid: 21304985
references.citation: J Acquir Immune Defic Syndr. 2006 Mar;41(3):352-60
references.pmid: 16540937
references.citation: PLoS One. 2009 Dec 03;4(12):e8153
references.pmid: 19997510
references.citation: J Acquir Immune Defic Syndr Hum Retrovirol. 1997 Mar 1;14(3):249-58
references.pmid: 9117458
references.citation: Viruses. 2010 Jan;2(1):33-54
references.pmid: 21994599
references.citation: AIDS. 2010 Apr 24;24(7):941-5
references.pmid: 20168202
references.citation: Proc Natl Acad Sci U S A. 2008 May 27;105(21):7552-7
references.pmid: 18490657
references.citation: Cochrane Database Syst Rev. 2012 Jul 11;(7):CD007189
references.pmid: 22786505
references.citation: J Infect Dis. 2007 Oct 15;196(8):1167-76
references.pmid: 17955435
references.citation: Antivir Ther. 2001 Sep;6(3):185-9
references.pmid: 11808753
references.citation: PLoS One. 2012;7(2):e31695
references.pmid: 22348121
references.citation: PLoS Med. 2012;9(7):e1001258
references.pmid: 22802738
references.citation: N Engl J Med. 2012 Aug 2;367(5):399-410
references.pmid: 22784037
references.citation: Epidemics. 2010 Jun;2(2):66-79
references.pmid: 21352777
references.citation: AIDS. 2009 Sep 10;23(14):F9-F17
references.pmid: 19644346
references.citation: PLoS Comput Biol. 2009 Oct;5(10):e1000505
references.pmid: 19855824
references.citation: Lancet Infect Dis. 2011 Jan;11(1):45-56
references.pmid: 21126914
references.citation: AIDS Rev. 2012 Jan-Mar;14(1):28-36
references.pmid: 22297502
references.citation: AIDS. 2010 May 15;24(8):1177-83
references.pmid: 20386427
references.citation: J Virol. 2009 Apr;83(8):3556-67
references.pmid: 19193811
references.citation: AIDS Res Hum Retroviruses. 2011 Jul;27(7):745-9
references.pmid: 21235402
references.citation: AIDS. 2011 Oct 23;25(16):2019-26
references.pmid: 21832936
references.citation: J Infect Dis. 2004 May 15;189(10):1785-92
references.pmid: 15122514
references.citation: J Infect Dis. 2012 Nov;206(9):1433-42
references.pmid: 22997233
references.citation: J Acquir Immune Defic Syndr. 2009 Aug 15;51(5):530-5
references.pmid: 19521252
references.citation: PLoS Pathog. 2010 May 06;6(5):e1000876
references.pmid: 20463808
references.citation: Science. 2010 Sep 3;329(5996):1168-74
references.pmid: 20643915
references.citation: PLoS One. 2012;7(9):e44819
references.pmid: 23024766
references.citation: Lancet. 2012 Jul 28;380(9839):367-77
references.pmid: 22819660
references.citation: AIDS. 2008 Nov 30;22(18):2509-15
references.pmid: 19005274
references.citation: J Infect Dis. 2011 Nov;204(9):1463-9
references.pmid: 21921202
references.citation: PLoS One. 2011;6(7):e22245
references.pmid: 21799802
references.citation: Arch Sex Behav. 2008 Oct;37(5):708-19
references.pmid: 18521734
references.citation: PLoS Med. 2008 Mar 18;5(3):e50
references.pmid: 18351795
references.citation: J Exp Med. 2009 Jun 8;206(6):1273-89
references.pmid: 19487424
references.citation: N Engl J Med. 2011 May 19;364(20):1943-54
references.pmid: 21591946
references.citation: Nat Rev Genet. 2009 Aug;10(8):540-50
references.pmid: 19564871
references.citation: J Acquir Immune Defic Syndr. 2011 May 1;57(1):77-87
references.pmid: 21297479
references.citation: AIDS. 2012 Jun 1;26(9):1121-9
references.pmid: 22333750
references.citation: AIDS. 1994 Jun;8(6):837-41
references.pmid: 8086144
references.citation: J Virol. 2012 Mar;86(5):2715-28
references.pmid: 22190722
references.citation: J Adv Nurs. 2001 Feb;33(3):357-70
references.pmid: 11251723
references.citation: AIDS. 2012 Sep 10;26(14):1813-22
references.pmid: 22739398
references.citation: Curr Opin HIV AIDS. 2010 Jul;5(4):277-82
references.pmid: 20543601
references.citation: AIDS. 2003 Jan 3;17(1):F1-5
references.pmid: 12478089
references.citation: PLoS Pathog. 2011 Sep;7(9):e1002209
references.pmid: 21980282
references.citation: PLoS One. 2011 Mar 10;6(3):e16902
references.pmid: 21423744
references.citation: J Theor Biol. 2009 Nov 21;261(2):341-60
references.pmid: 19660475
references.citation: AIDS. 2011 Jan 14;25(2):211-20
references.pmid: 21124202
references.citation: PLoS One. 2011;6(9):e25286
references.pmid: 21966483
references.citation: AIDS Res Hum Retroviruses. 2007 Dec;23(12):1569-74
references.pmid: 18160015
references.citation: Ann N Y Acad Sci. 2011 Aug;1230:108-18
references.pmid: 21824168