Application of a case-control study design to investigate genotypic signatures of HIV-1 transmission

Retrovirology

Volumn 9, Issue , 2012, Pages

  Mota, Talia M ^a   Murray, John M ^b,c   Center, Rob J ^a   Purcell, Damian F J ^a   McCaw, James M ^d,e  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

^c UNIVERSITY OF NEW SOUTH WALES   (Australia)

^d ROYAL CHILDREN'S HOSPITAL   (Australia)

^e UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

4 7; Case control study; Chronic infection; Envelope protein; Glycosites; Histidine; HIV 1; Transmission; Variable loops

Indexed keywords

HISTIDINE; VIRUS ENVELOPE PROTEIN;

ARTICLE; BINDING SITE; BOTTLENECK POPULATION; CASE CONTROL STUDY; CONTROLLED STUDY; GENOTYPING TECHNIQUE; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; NUCLEOTIDE SEQUENCE; PREVALENCE; PROMOTER REGION; UNINDEXED SEQUENCE; VIRUS STRAIN; VIRUS TRANSMISSION;

AMINO ACID SEQUENCE; BINDING SITES; CASE-CONTROL STUDIES; CONSENSUS SEQUENCE; GENETIC VARIATION; GENOTYPING TECHNIQUES; HISTIDINE; HIV ENVELOPE PROTEIN GP120; HIV INFECTIONS; HIV-1; HUMANS; INTEGRINS; LOGISTIC MODELS; MOLECULAR SEQUENCE DATA; ODDS RATIO; PROTEIN SORTING SIGNALS; SPECIES SPECIFICITY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84862618179     PISSN: None     EISSN: 17424690     Source Type: Journal    
DOI: 10.1186/1742-4690-9-54     Document Type: Article

References (31)

1. Gnanakaran S, Bharracharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom F, Anderson J, Ping L-H, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, DeCamp AC, Magaret CA, Schief WR, Ban Y-E A, Zhang M, Soderberg KA, Sodroski JG, Haynew BF, Shaw GM, Hahn BH, Korber B. Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog 2011, 7(9):e1002209. 10.1371/journal.ppat.1002209, 3182927, 21980282.
2. Asmal M, Hellmann I, Lie W, Keele BF, Perelson AS, Bhattacharya T, Gnanakaran S, Daniels M, Haynes BF, Korber BT, Haha BH, Shaw GM, Letvin NL. A Signature in HIV-1 envelope leader peptide associated with transition from acute to chronic infection impacts envelope processing and infectivity. PLoS ONE 2011, 6:e23673. 10.1371/journal.pone.0023673, 3158090, 21876761.
3. Haaland RE, Hawkins PA, Salazar-Gonzalez J, Johnson A, Tichacek A, Karita E, Manigart O, Mulenga J, Keele BF, Shaw GM, Hahn BH, Allen S, Derdeyn CA, Hunter E. Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1. PLoS Pathog 2009, 5:e1000274. 10.1371/journal.ppat.1000274, 2621345, 19165325.
4. Derdeyn CA, Kecker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, Denham SA, Heil ML, Kasolo F, Musonda R, Hahn B, Shaw G, Korber BT, Allen S, Hunter E. Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 2004, 303:2019-2022. 10.1126/science.1093137, 15044802.
5. Chohan B, Lang D, Sagar M, Korber B, Lavreys L, Richardson B, Overbaugh J. Selection for human immunodeficiency virus type 1 evnelope glycosylation variants with shorter V1-V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels. Virology 2005, 79(10):6528-6531. Slides with audio can be accessed: http://pag.aids2010.org/flash/?pid=100868..
6. Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, Wei X, Jiang C, Kirchherr JL, Gao F, Anderson JA, Ping L-H, Swanstrom R, Tomaras GD, Blattner WA, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Cohen MS, Montefiori DC, Haynes BF, Gaschen B, Athreya GS, Lee HY, Woo N, Seoighe C, Perelson AS, Bhattacharya T, Korber BT, Hahn BH, Shaw GM. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci 2008, 105:7552-7557. 10.1073/pnas.0802203105, 2387184, 18490657.
7. Abrahams MR, Anderson JA, Giorgi EE, Seoighe C, Mlisana K, Ping L-H, Athreya GS, Treurnicht FK, Keele BF, Wood N, Salazar-Gonzalez JF, Bhattacharya T, Chu H, Hoffman I, Galvin S, Mapanje C, Kazembe P, Thebus R, Fiscus S, Hide W, Cohen MS, Abdool Kaim S, Haynes BF, Shaw GM, Hahn BH, Korber BT, Swanstrom R, Williamson C. Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distriution of transmitted variants. J Virol 2009, 83(8):3556. 10.1128/JVI.02132-08, 2663249, 19193811.
8. Salazar-Gonzalez JF, Salazar MG, Keele BF, Learn GH, Giorgi EE, Li H, Decker JM, Wang S, Baalwa J, Kraus MH, Parrish NF, Ochsenbauer-Jambor C, Kappes JC, Saag MS, Cohen MS, Mulenga J, Derdeyn CA, Allen S, Hunter E, Markowitz M, Hraber R, Perelson AS, Bhattacharya T, Haynes BF, Korber BT, Hahn BH, Shaw GM. Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J Exp Med 2009, 206(6):1273-1289. 10.1084/jem.20090378, 2715054, 19487424.
9. Sagar M, Laeyendecker O, Lee S, Gamiel J, Wawr MJ, Gray RH, Serwadda D, Sewankambo NK, Shepherd JC, Toma J, Huang W, Quinn T. Selection of HIV variants with signature genotypic characteristics during hetersexual transmission. JID 2009, 199:580-589. 10.1086/596557, 2755256, 19143562.
10. Sagar M, Kirkegaard E, Lavreys L, Overbaugh J. Diversity in HIV-1 Envelope V1-V3 sequences early in infection reflects sequences diversity throughout the HIV-1 genome but down not predict the extent of sequence diversity during chronic infection. AIDS Research and Human Retroviruses 2006, 22(5):430-437. 10.1089/aid.2006.22.430, 16706620.
11. Nawaz F, Cicala C, Van Ryk D, Block KE, Jelicic K, McNally JP, Ogundare O, Pascuccio M, Patel N, Wie D, Fauci AS, Arthos J. The genotype of early-transmitting HIV gp120s promotes α4β7-reactivity, revealing α4β7+/CD4+ T cells as key targets in mucosal transmission. PLoS Pathog 2011, 7(2):e1001301. 10.1371/journal.ppat.1001301, 3044691, 21383973.
12. Ritola K, Pilcher C, Fiscus S, Hoffman NG, Nelson JAE, Kitrinos KM, Hicks CB, Eron JJ, Swanstorm R. Multiple V1/V2 env variants re frequently present during primary infection with human immunodeficiency virus type 1. Virology 2004, 78(20):11208-11218.
13. Wood N, Bhattacharya T, Keele BF, Giorgi E, Lie M, Gaschen B, Daniels M, Ferrari G, Haynes BF, McMichael A, Shaw G, Hahn BA, Korber B, Seoighe C. HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC. PLoS Pathogens 2009, 5(5):e1000414. 10.1371/journal.ppat.1000414, 2671846, 19424423.
14. Keele BF, Derdeyn C. Genetic and antigenic features of the transmitted virus. Curr Opin HIV AIDS 2009, 4:352-357. 10.1097/COH.0b013e32832d9fef, 20048697.
15. Anthony F. New Concepts in HIV/AIDS Pathogenesis: Implications for Interventions. XVIII International AIDS Conference 2010, Vienna, Slides with audio can be accessed: http://pag.aids2010.org/flash/?pid=100868..
16. Derdeyn CA, Hunter E. Viral characteristics of transmitted HIV. Curr Opin HIV AIDS 2009, 3:16-21.
17. Keele BF. Identifying and characterizing recently transmitted viruses. Curr Opin HIV AIDS 2010, 5:327-334. 10.1097/COH.0b013e32833a0b9b, 2914479, 20543609.
18. Frost SDW, Liu Y, Kosakovsky Pond SL, Chappey C, Wrin T, Petropoulos CJ, Little SJ, Richman DD. J Virol 2005, 79(10):6523. 10.1128/JVI.79.10.6523-6527.2005, 1091710, 15858036.
19. Liu Y, Curlin ME, Diem K, Zhao H, Ghosh AK, Zhu H, Woodward AS, Maenza J, Stevens CE, Stekler J, Collier AC, Genowati I, Deng W, Zioni R, Corey L, Zhu T, Mullins JI. Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B viruses. Virology 2008, 347:229-233.
20. Los Alamos National Laboratories. Los Alamos HIV Sequence Database http://www.hiv.lanl.gov/ Operated by Los Alamos National Security, LLC, for the U.S. Department of Energy's National Nuclear Security Administration.
21. Cicala C, Martinelli E, McNally J, Goode DJ, Gopaul R, Hiatt J, Jelicic K, Kottilil S, Macleod K, O'Shea A, Patel N, Van Ryk D, Wie D, Pascuccio M, Ling Y, McKinnon L, Izulla P, Kimani J, Kaul R, Fauci AS, Arthos J. The integrin α4β7 forms a complex with cell-surface CD4 and defines a T-cell subset that is highly susceptible to infection by HIV-1. December 2009, 106(49):20877-20882.
22. Cicala C, Arthos J, Fauci A. HIV-1 envelope, integrins and co-receptor use in mucosal transmission of HIV. J Transl Med 2011, 9(Suppl 1):S2. 3105502, 21284901.
23. Arthos J, Cicala C, Martinelli E, Macleod K, Van Ryk D, Wie D, Xiao Z, Veenstra TD, Conrad TP, Lempicki RA, McLaughlin S, Pascuccio M, Gopaul R, McNally J, Cruz CC, Censoplano N, Chung E, Reitano KN, Kottilil S, Goode DJ, Fauci AS. HIV-1 envelope protein binds to and signals through integrin α4β7, the gut mucosal homing receptor for peripheral T cells. Nat Immunol 2008, 9(3):301-309. 10.1038/ni1566, 18264102.
24. von Andrian UH. CR Mackay. T-cell function and migration. Two sides of the same coin. N Engl J Med 2000, 343:1020-1034. 10.1056/NEJM200010053431407, 11018170.
25. Webb P, Bain C, Pirozzo S. Essential Epidemiology: and introduction for Students and Health Professionals 2005, Cambridge University Press, New York.
26. Kirkwood BR, Sterne JAC. Medical Statistics 2003, Blackwell Science, Inc, Oxford, 2.
27. Leonard CK, Spellman MW, Riddle L, Harris RJ, Thomas JN, Gregory TJ, et al. Assignment of intrachain disulfide bonds and characterization of potential glycosylation sites of the type 1 recombinant human immunodeficiency virus envelope glycoprotein (gp120) expressed in chinese hamster ovary cells. J Biological Chemistry 1990, 265(18):10373-10382.
28. Binley JM, Ban Y-E A, Crooks ET, Eggink D, Osawa K, Schief WR, Sanders RW. Role of complex carbohydrates in human immunodeficiency virus type 1 infection and resistance to antibody neutralization. J of Virology 2010, 84(11):5637-5655.
29. Rieder P, Joos B, Scherrer AU, Kuster H, Braun D, Grube C, Niederost B, Leemann C, Gianella S, Metzner KJ, Boni J, Weber R, Gunthard HF. Characterization of human immunodficiency virus type 1 (HIV-1) diversity and tropism in 145 patients with primary HIV-1 infection. Clin Infect Dis 2011, 53(12):1271-9. 10.1093/cid/cir725, 21998286.
30. Hedskog C, Mild M, Albert J. Transmission of the X4 Phenotype of HIV-1: Is there evidence against the " Random Transmission" hypothesis?. J Infect Dis 2012, 205:163-5. 10.1093/infdis/jir719, 22147793.
31. Korber BT, Foley BT, Kuiken CL, Pillai SK, Sodroski JG. Numbering Positions in HIV Relative to HXB2CG. Human Retroviruses and AIDS 1998 Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, Korber B, Kuiken CL, Foley B, Hahn B, McCutchan F, Mellors JW, Sodroski J, pp. III-102-111.