Genital Tract Sequestration of SIV following Acute Infection

1. PilcherCD

ShugarsDC

FiscusSA

MillerWC

MenezesP

2001 HIV in body fluids during primary HIV infection: implications for pathogenesis, treatment and public health. Aids 15 837 845

2. PilcherH

2004 Snapshot of a pandemic. Nature 430 134 135

3. PilcherCD

EronJJJr

VemazzaPL

BattegayM

HarrT

2001 Sexual transmission during the incubation period of primary HIV infection. Jama 286 1713 1714

4. QuinnTC

WawerMJ

SewankamboN

SerwaddaD

LiC

2000 Viral load and heterosexual transmission of human immunodeficiency virus type 1. Rakai Project Study Group. N Engl J Med 342 921 929

5. GrayRH

WawerMJ

BrookmeyerR

SewankamboNK

SerwaddaD

2001 Probability of HIV-1 transmission per coital act in monogamous, heterosexual, HIV-1-discordant couples in Rakai, Uganda. Lancet 357 1149 1153

6. WhitneyJB

LuedemannC

HraberP

RaoSS

MascolaJR

2009 T cell vaccination reduces SIV in semen. J Virol 83 20 10840 3

7. PilcherCD

TienHC

EronJJJr

VernazzaPL

LeuSY

2004 Brief but efficient: acute HIV infection and the sexual transmission of HIV. J Infect Dis 189 1785 1792

8. CoffinJM

1995 HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267 483 489

9. NowakM

1990 HIV mutation rate. Nature 347 522

10. KemalKS

FoleyB

BurgerH

AnastosK

MinkoffH

2003 HIV-1 in genital tract and plasma of women: compartmentalization of viral sequences, coreceptor usage, and glycosylation. Proc Natl Acad Sci U S A 100 12972 12977

11. EronJJ

VernazzaPL

JohnstonDM

Seillier-MoiseiwitschF

AlcornTM

1998 Resistance of HIV-1 to antiretroviral agents in blood and seminal plasma: implications for transmission. Aids 12 F181 189

12. GuptaP

LerouxC

PattersonBK

KingsleyL

RinaldoC

2000 Human immunodeficiency virus type 1 shedding pattern in semen correlates with the compartmentalization of viral Quasi species between blood and semen. J Infect Dis 182 79 87

13. PolesMA

ElliottJ

VingerhoetsJ

MichielsL

ScholliersA

2001 Despite high concordance, distinct mutational and phenotypic drug resistance profiles in human immunodeficiency virus type 1 RNA are observed in gastrointestinal mucosal biopsy specimens and peripheral blood mononuclear cells compared with plasma. J Infect Dis 183 143 148

14. KiesslingAA

FitzgeraldLM

ZhangD

ChhayH

BrettlerD

1998 Human immunodeficiency virus in semen arises from a genetically distinct virus reservoir. AIDS Res Hum Retroviruses 14 Suppl 1 S33 41

15. ByrnRA

ZhangD

EyreR

McGowanK

KiesslingAA

1997 HIV-1 in semen: an isolated virus reservoir. Lancet 350 1141

16. PhilpottS

BurgerH

TsoukasC

FoleyB

AnastosK

2005 Human immunodeficiency virus type 1 genomic RNA sequences in the female genital tract and blood: compartmentalization and intrapatient recombination. J Virol 79 353 363

17. DelwartEL

MullinsJI

GuptaP

LearnGHJr

HolodniyM

1998 Human immunodeficiency virus type 1 populations in blood and semen. J Virol 72 617 623

18. DiemK

NickleDC

MotoshigeA

FoxA

RossS

2008 Male genital tract compartmentalization of human immunodeficiency virus type 1 (HIV). AIDS Res Hum Retroviruses 24 561 571

19. ParanjpeS

CraigoJ

PattersonB

DingM

BarrosoP

2002 Subcompartmentalization of HIV-1 quasispecies between seminal cells and seminal plasma indicates their origin in distinct genital tissues. AIDS Res Hum Retroviruses 18 1271 1280

20. Shehu-XhilagaM

de KretserD

Dejucq-RainsfordN

HedgerM

2005 Standing in the way of eradication: HIV-1 infection and treatment in the male genital tract. Curr HIV Res 3 345 359

21. RouletV

SatieAP

RuffaultA

Le TortorecA

DenisH

2006 Susceptibility of human testis to human immunodeficiency virus-1 infection in situ and in vitro. Am J Pathol 169 2094 2103

22. RouletV

DenisH

StaubC

Le TortorecA

DelaleuB

2006 Human testis in organotypic culture: application for basic or clinical research. Hum Reprod 21 1564 1575

23. Le TortorecA

SatieAP

DenisH

Rioux-LeclercqN

HavardL

2008 Human prostate supports more efficient replication of HIV-1 R5 than X4 strains ex vivo. Retrovirology 5 119

24. Le TortorecA

Le GrandR

DenisH

SatieAP

ManniouiK

2008 Infection of semen-producing organs by SIV during the acute and chronic stages of the disease. PLoS One 3 e1792

25. Le TortorecA

DenisH

SatieAP

PatardJJ

RuffaultA

2008 Antiviral responses of human Leydig cells to mumps virus infection or poly I:C stimulation. Hum Reprod 23 2095 2103

26. Le TortorecA

Dejucq-RainsfordN

2009 HIV infection of the male genital tract - consequences for sexual transmission and reproduction. Int J Androl 33 e98 e108

27. Le TortorecA

Dejucq-RainsfordN

2007 [The male genital tract: A host for HIV]. Gynecol Obstet Fertil 35 1245 1250

28. Dejucq-RainsfordN

JegouB

2004 Viruses in semen and male genital tissues–consequences for the reproductive system and therapeutic perspectives. Curr Pharm Des 10 557 575

29. MillerCJ

VogelP

AlexanderNJ

DandekarS

HendrickxAG

1994 Pathology and localization of simian immunodeficiency virus in the reproductive tract of chronically infected male rhesus macaques. Lab Invest 70 255 262

30. ByrnRA

KiesslingAA

1998 Analysis of human immunodeficiency virus in semen: indications of a genetically distinct virus reservoir. J Reprod Immunol 41 161 176

31. GhosnJ

ChaixML

PeytavinG

ReyE

BressonJL

2004 Penetration of enfuvirtide, tenofovir, efavirenz, and protease inhibitors in the genital tract of HIV-1-infected men. Aids 18 1958 1961

32. KroodsmaKL

KozalMJ

HamedKA

WintersMA

MeriganTC

1994 Detection of drug resistance mutations in the human immunodeficiency virus type 1 (HIV-1) pol gene: differences in semen and blood HIV-1 RNA and proviral DNA. J Infect Dis 170 1292 1295

33. SmithDM

WongJK

ShaoH

HightowerGK

MaiSH

2007 Long-term persistence of transmitted HIV drug resistance in male genital tract secretions: implications for secondary transmission. J Infect Dis 196 356 360

34. PingLH

CohenMS

HoffmanI

VernazzaP

Seillier-MoiseiwitschF

2000 Effects of genital tract inflammation on human immunodeficiency virus type 1 V3 populations in blood and semen. J Virol 74 8946 8952

35. ZhuT

WangN

CarrA

NamDS

Moor-JankowskiR

1996 Genetic characterization of human immunodeficiency virus type 1 in blood and genital secretions: evidence for viral compartmentalization and selection during sexual transmission. J Virol 70 3098 3107

36. PilcherCD

JoakiG

HoffmanIF

MartinsonFE

MapanjeC

2007 Amplified transmission of HIV-1: comparison of HIV-1 concentrations in semen and blood during acute and chronic infection. Aids 21 1723 1730

37. PilcherCD

PriceMA

HoffmanIF

GalvinS

MartinsonFE

2004 Frequent detection of acute primary HIV infection in men in Malawi. Aids 18 517 524

38. TindallB

EvansL

CunninghamP

McQueenP

HurrenL

1992 Identification of HIV-1 in semen following primary HIV-1 infection. Aids 6 949 952

39. RitolaK

PilcherCD

FiscusSA

HoffmanNG

NelsonJA

2004 Multiple V1/V2 env variants are frequently present during primary infection with human immunodeficiency virus type 1. J Virol 78 11208 11218

40. ZhangL

RoweL

HeT

ChungC

YuJ

2002 Compartmentalization of surface envelope glycoprotein of human immunodeficiency virus type 1 during acute and chronic infection. J Virol 76 9465 9473

41. NunnariG

OteroM

DornadulaG

VanellaM

ZhangH

2002 Residual HIV-1 disease in seminal cells of HIV-1-infected men on suppressive HAART: latency without on-going cellular infections. Aids 16 39 45

42. KalichmanSC

Di BertoG

EatonL

2008 Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. Sex Transm Dis 35 55 60

43. ZarateS

PondSL

ShapshakP

FrostSD

2007 Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. J Virol 81 6643 6651

44. WhitneyJB

LuedemannC

HraberP

RaoSS

MascolaJR

2009 T-cell vaccination reduces simian immunodeficiency virus levels in semen. J Virol 83 10840 10843

45. KeeleBF

LiH

LearnGH

HraberP

GiorgiEE

2009 Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1. J Exp Med 206 1117 1134

46. ZhangM

GaschenB

BlayW

FoleyB

HaigwoodN

2004 Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin. Glycobiology 14 1229 1246

47. Kosakovsky PondSL

FrostSD

2005 Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22 1208 1222

48. Kosakovsky PondSL

PosadaD

GravenorMB

WoelkCH

FrostSD

2006 GARD: a genetic algorithm for recombination detection. Bioinformatics 22 3096 3098

49. PillaiSK

GoodB

PondSK

WongJK

StrainMC

2005 Semen-specific genetic characteristics of human immunodeficiency virus type 1 env. J Virol 79 1734 1742

50. ButlerDM

DelportW

Kosakovsky PondSL

LakdawalaMK

ChengPM

2010 The origins of sexually transmitted HIV among men who have sex with men. Sci Transl Med 2 18re11

51. BhattacharyaT

DanielsM

HeckermanD

FoleyB

FrahmN

2007 Founder effects in the assessment of HIV polymorphisms and HLA allele associations. Science 315 1583 1586

52. SlatkinM

MaddisonWP

1990 Detecting isolation by distance using phylogenies of genes. Genetics 126 249 260

53. PondSL

FrostSD

MuseSV

2005 HyPhy: hypothesis testing using phylogenies. Bioinformatics 21 676 679

54. BullME

LearnGH

McElhoneS

HittiJ

LockhartD

2009 Monotypic human immunodeficiency virus type 1 genotypes across the uterine cervix and in blood suggest proliferation of cells with provirus. J Virol 83 6020 6028

55. BullM

LearnG

GenowatiI

McKernanJ

HittiJ

2009 Compartmentalization of HIV-1 within the female genital tract is due to monotypic and low-diversity variants not distinct viral populations. PLoS One 4 e7122

56. Kosakovsky PondSL

PosadaD

GravenorMB

WoelkCH

FrostSD

2006 Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol 23 1891 1901

57. Salazar-GonzalezJF

SalazarMG

KeeleBF

LearnGH

GiorgiEE

2009 Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J Exp Med 206 1273 1289

58. KeeleBF

GiorgiEE

Salazar-GonzalezJF

DeckerJM

PhamKT

2008 Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A 105 7552 7557

59. PalmerS

KearneyM

MaldarelliF

HalvasEK

BixbyCJ

2005 Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J Clin Microbiol 43 406 413

60. Salazar-GonzalezJF

BailesE

PhamKT

SalazarMG

GuffeyMB

2008 Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. J Virol 82 3952 3970

61. LiuSLRA

ShankarappaR

LearnGH

HsuL

DavidovO

1996 HIV quasispecies and resampling. Science 273 415 416

62. ZhuJ

HladikF

WoodwardA

KlockA

PengT

2009 Persistence of HIV-1 receptor-positive cells after HSV-2 reactivation is a potential mechanism for increased HIV-1 acquisition. Nat Med 15 886 892

63. CelumC

WaldA

LingappaJR

MagaretAS

WangRS

2010 Acyclovir and transmission of HIV-1 from persons infected with HIV-1 and HSV-2. N Engl J Med 362 427 439

64. RiegG

ButlerDM

SmithDM

DaarES

2010 Seminal plasma HIV levels in men with asymptomatic sexually transmitted infections. Int J STD AIDS 21 207 208

65. CohenMS

HoffmanIF

RoyceRA

KazembeP

DyerJR

1997 Reduction of concentration of HIV-1 in semen after treatment of urethritis: implications for prevention of sexual transmission of HIV-1. AIDSCAP Malawi Research Group. Lancet 349 1868 1873

66. HaalandRE

HawkinsPA

Salazar-GonzalezJ

JohnsonA

TichacekA

2009 Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1. PLoS Pathog 5 e1000274

67. DerdeynCA

DeckerJM

Bibollet-RucheF

MokiliJL

MuldoonM

2004 Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 303 2019 2022

68. HarrisonRM

1980 Semen parameters in Macaca mulatta: ejaculates from random and selected monkeys. J Med Primatol 9 265 273

69. ClineAN

BessJW

PiatakMJr

LifsonJD

2005 Highly sensitive SIV plasma viral load assay: practical considerations, realistic performance expectations, and application to reverse engineering of vaccines for AIDS. J Med Primatol 34 303 312

70. WhitneyJB

LuedemannC

BaoS

MiuraA

RaoSS

2009 Monitoring HIV vaccine trial participants for primary infection: studies in the SIV/macaque model. Aids 23 1453 1460

71. DouekDC

BrenchleyJM

BettsMR

AmbrozakDR

HillBJ

2002 HIV preferentially infects HIV-specific CD4+ T cells. Nature 417 95 98

72. MattapallilJJ

DouekDC

HillB

NishimuraY

MartinM

2005 Massive infection and loss of memory CD4+ T cells in multiple tissues during acute SIV infection. Nature 434 1093 1097

73. LearnGHJr

KorberBT

FoleyB

HahnBH

WolinskySM

1996 Maintaining the integrity of human immunodeficiency virus sequence databases. J Virol 70 5720 5730

74. GilbertPB

RossiniAJ

ShankarappaR

2005 Two-sample tests for comparing intra-individual genetic sequence diversity between populations. Biometrics 61 106 117

75. ParadisE

ClaudeJ

StrimmerK

2004 APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20 289 290

76. GascuelO

1997 BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14 685 695

77. GuindonS

GascuelO

2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52 696 704

78. KulkarniSS

LapedesA

TangH

GnanakaranS

DanielsMG

2009 Highly complex neutralization determinants on a monophyletic lineage of newly transmitted subtype C HIV-1 Env clones from India. Virology 385 505 520