Role of donor genital tract HIV-1 diversity in the transmission bottleneck

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 46, 2011, Pages

  Boeras, Debrah I ^a   Hraber, Peter T ^b   Hurlston, Mackenzie ^a   Evans Strickfaden, Tammy ^c   Bhattacharya, Tanmoy ^b   Giorgi, Elena E ^b   Mulenga, Joseph ^d   Karita, Etienne ^e   Korber, Bette T ^b   Allen, Susan ^a   Hart, Clyde E ^c   Derdeyn, Cynthia A ^a   Hunter, Eric ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^d Zambia Emory HIV Research Project   (Zambia)

^e Projet San Francisco   (Rwanda)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; CLINICAL ARTICLE; DONOR; FEMALE; GENETIC VARIABILITY; GENITAL SYSTEM; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RWANDA; SEXUAL TRANSMISSION; VIRUS ENVELOPE; VIRUS TRANSMISSION; ZAMBIA;

DNA, VIRAL; FALSE POSITIVE REACTIONS; FEMALE; GENITALIA, FEMALE; HIV INFECTIONS; HIV SEROPOSITIVITY; HIV-1; HUMANS; LONGITUDINAL STUDIES; MALE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, GENETIC; RWANDA; SEXUAL BEHAVIOR; TIME FACTORS; ZAMBIA;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 81755187039     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1103764108     Document Type: Article

References (47)

1. UNAIDS (2010) Global report 2010, Geneva. Available at http://www.unaids.org/glovalreport/documents/20101123-GlovalReport-full-en.pdf. Accessed November, 2010.
2. Delwart EL, et al. (1998) Human immunodeficiency virus type 1 populations in blood and semen. J Virol 72:617-623. (Pubitemid 28048879)
3. Gupta P, et al. (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. (Pubitemid 30497791)
4. Paranjpe S, et al. (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. (Pubitemid 36042987)
5. Zhu T, et al. (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. (Pubitemid 26121927)
6. Overbaugh J, Anderson RJ, Ndinya-Achola JO, Kreiss JK (1996) Distinct but related human immunodeficiency virus type 1 variant populations in genital secretions and blood. AIDS Res Hum Retroviruses 12:107-115. (Pubitemid 26039709)
7. Poss M, et al. (1995) Diversity in virus populations from genital secretions and peripheral blood from women recently infected with human immunodeficiency virus type 1. J Virol 69:8118-8122.
8. Sagar M, et al. (2004) Human immunodeficiency virus type 1 (HIV-1) diversity at time of infection is not restricted to certain risk groups or specific HIV-1 subtypes. J Virol 78:7279-7283. (Pubitemid 38781567)
9. Derdeyn CA, et al. (2004) Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 303:2019-2022. (Pubitemid 38393277)
10. Haaland RE, et al. (2009) Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1. PLoS Pathog 5:e1000274.
11. Keele BF, et al. (2008) Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci USA 105:7552-7557. (Pubitemid 351830056)
12. Ritola K, et al. (2004) Multiple V1/V2 env variants are frequently present during primary infection with human immunodeficiency virus type 1. J Virol 78:11208-11218. (Pubitemid 39299660)
13. Frost SD, et al. (2005) Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J Virol 79:6523-6527. (Pubitemid 40617256)
14. Salazar-Gonzalez JF, et al. (2008) Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. J Virol 82:3952-3970. (Pubitemid 351521232)
15. Abrahams MR, et al.; CAPRISA Acute Infection Study Team; Center for HIV-AIDS Vaccine Immunology Consortium (2009) Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-Poisson distribution of transmitted variants. J Virol 83:3556-3567.
16. Fischer W, et al. (2010) Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS ONE 5:e12303.
17. Ellerbrock TV, et al. (2001) Cellular replication of human immunodeficiency virus type 1 occurs in vaginal secretions. J Infect Dis 184:28-36. (Pubitemid 32568497)
18. Anderson JA, et al.; Center for HIV/AIDS Vaccine Immunology (2010) HIV-1 populations in semen arise through multiple mechanisms. PLoS Pathog 6:e1001053.
19. Bull M, et al. (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.
20. Diem K, et al. (2008) Male genital tract compartmentalization of human immunodeficiency virus type 1 (HIV). AIDS Res Hum Retroviruses 24:561-571. (Pubitemid 351571032)
21. Nickle DC, et al. (2003) Evolutionary indicators of human immunodeficiency virus type 1 reservoirs and compartments. J Virol 77:5540-5546. (Pubitemid 36460971)
22. Whitney JB, et al. (2011) Genital tract sequestration of SIV during acute infection. PLoS Pathog 7:e1001293.
23. Slatkin M, Maddison WP (1989) A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123:603-613. (Pubitemid 19274683)
24. Poss M, et al. (1998) Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. J Virol 72:8240-8251. (Pubitemid 28421821)
25. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100:9440-9445. (Pubitemid 37033947)
26. Byrn RA, Kiessling AA (1998) Analysis of human immunodeficiency virus in semen: Indications of a genetically distinct virus reservoir. J Reprod Immunol 41:161-176. (Pubitemid 29017873)
27. Byrn RA, Zhang D, Eyre R, McGowan K, Kiessling AA (1997) HIV-1 in semen: An isolated virus reservoir. Lancet 350:1141. (Pubitemid 27454008)
28. Coombs RW, et al. (1998) Association between culturable human immunodeficiency virus type 1 (HIV-1) in semen and HIV-1 RNA levels in semen and blood: Evidence for compartmentalization of HIV-1 between semen and blood. J Infect Dis 177:320-330. (Pubitemid 28063755)
29. Pillai SK, et al. (2005) Semen-specific genetic characteristics of human immunodeficiency virus type 1 env. J Virol 79:1734-1742. (Pubitemid 40459119)
30. Ping LH, et al. (2000) Effects of genital tract inflammation on human immunodeficiency virus type 1 V3 populations in blood and semen. J Virol 74: 8946-8952.
31. Chohan B, et al. (2005) Selection for human immunodeficiency virus type 1 envelope glycosylation variants with shorter V1-V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels. J Virol 79:6528-6531. (Pubitemid 40617257)
32. Go EP, et al. (2011) Characterization of glycosylation profiles of HIV-1 transmitted/ founder envelopes by mass spectrometry. J Virol 85:8270-8284.
33. Liu Y, et al. (2008) Env length and N-linked glycosylation following transmission of human immunodeficiency virus type 1 subtype B viruses. Virology 374:229-233.
34. Nawaz F, et al. (2011) The genotype of early-transmitting HIV gp120s promotes α (4) β(7)-reactivity, revealing α (4) β(7) +/CD4+ T cells as key targets in mucosal transmission. PLoS Pathog 7:e1001301.
35. Chomba E, et al., Rwanda Zambia HIV Research Group (2008) Evolution of couples' voluntary counseling and testing for HIV in Lusaka, Zambia. J Acquir Immune Defic Syndr 47:108-115. (Pubitemid 351619377)
36. McKenna SL, et al. (1997) Rapid HIV testing and counseling for voluntary testing centers in Africa. AIDS 11(Suppl 1):S103-S110. (Pubitemid 27460100)
37. Fideli US, et al.; (2001) Virologic and immunologic determinants of heterosexual transmission of human immunodeficiency virus type 1 in Africa. AIDS Res Hum Retroviruses 17:901-910.
38. Allen S, et al. (1992) Effect of serotesting with counselling on condom use and seroconversion among HIV discordant couples in Africa. BMJ 304:1605-1609.
39. Dunkle KL, et al. (2008) New heterosexually transmitted HIV infections in married or cohabiting couples in urban Zambia and Rwanda: An analysis of survey and clinical data. Lancet 371:2183-2191. (Pubitemid 351885039)
40. Delany S, et al. (2008) Comparison of cervicovaginal lavage, cervicovaginal lavage enriched with cervical swab, and vaginal tampon for the detection of HIV-1 RNA and HSV-2 DNA in genital secretions. J Acquir Immune Defic Syndr 49:406-409.
41. Lorello G, et al. (2009) Discordance in HIV-1 viral loads and antiretroviral drug concentrations comparing semen and blood plasma. HIV Med 10:548-554.
42. Trask SA, et al. (2002) Molecular epidemiology of human immunodeficiency virus type 1 transmission in a heterosexual cohort of discordant couples in Zambia. J Virol 76:397-405. (Pubitemid 33139024)
43. Simmonds P, Balfe P, Ludlam CA, Bishop JO, Brown AJ (1990) Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1. J Virol 64:5840-5850.
44. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704. (Pubitemid 37365050)
45. Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD (2006) Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol 23:1891-1901. (Pubitemid 44412875)
46. Hudson RR (2000) A new statistic for detecting genetic differentiation. Genetics 155:2011-2014.
47. Zárate S, Pond SL, Shapshak P, Frost SD (2007) Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. J Virol 81:6643-6651. (Pubitemid 46878068)