HIV-1 subtype C envelope characteristics associated with divergent rates of chronic disease progression

Retrovirology

Volumn 7, Issue , 2010, Pages

  Archary, Derseree ^a   Gordon, Michelle L ^a   Green, Taryn N ^a   Coovadia, Hoosen M ^a   Goulder, Philip J R ^a,b   Ndung'u, Thumbi ^a  

^a UNIVERSITY OF KWAZULU NATAL   (South Africa)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPROTEIN GP 160; GLYCOPROTEIN GP 41; GP41 PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1;

ADULT; AMINO ACID SEQUENCE; ARTICLE; CLINICAL ARTICLE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DISEASE COURSE; FEMALE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; MALE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN GLYCOSYLATION; VIRUS ENVELOPE; VIRUS GENOME; CHEMICAL STRUCTURE; CHEMISTRY; CHRONIC DISEASE; COHORT ANALYSIS; GENETIC POLYMORPHISM; GENETICS; GLYCOSYLATION; HOST PATHOGEN INTERACTION; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; METABOLISM; MIDDLE AGED; MOLECULAR GENETICS; VIROLOGY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

CHRONIC DISEASE; COHORT STUDIES; DISEASE PROGRESSION; GLYCOSYLATION; HIV ENVELOPE PROTEIN GP160; HIV ENVELOPE PROTEIN GP41; HIV INFECTIONS; HIV-1; HOST-PATHOGEN INTERACTIONS; HUMANS; MALE; MIDDLE AGED; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; YOUNG ADULT;

EID: 78649502657     PISSN: None     EISSN: 17424690     Source Type: Journal    
DOI: 10.1186/1742-4690-7-92     Document Type: Article

References (54)

1. Mansky LM, Temin HM. Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J Virol 1995, 69:5087-5094. 189326, 7541846.
2. Preston BD, Poiesz BJ, Loeb LA. Fidelity of HIV-1 reverse transcriptase. Science 1988, 242:1168-1171. 10.1126/science.2460924, 2460924.
3. Brander C, Frahm N, Walker BD. The challenges of host and viral diversity in HIV vaccine design. Curr Opin Immunol 2006, 18:430-437. 10.1016/j.coi.2006.05.012, 16777397.
4. Walker BD, Burton DR. Toward an AIDS vaccine. Science 2008, 320:760-764. 10.1126/science.1152622, 18467582.
5. Resch W, Hoffman N, Swanstrom R. Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks. Virology 2001, 288:51-62. 10.1006/viro.2001.1087, 11543657.
6. Rademeyer C, Moore PL, Taylor N, Martin DP, Choge IA, Gray ES, Sheppard HW, Gray C, Morris L, Williamson C. Genetic characteristics of HIV-1 subtype C envelopes inducing cross-neutralizing antibodies. Virology 2007, 368:172-181. 10.1016/j.virol.2007.06.013, 17632196.
7. Wei X, Decker JM, Wang S, Hui H, Kappes JC, Wu X, Salazar-Gonzalez JF, Salazar MG, Kilby JM, Saag MS, et al. Antibody neutralization and escape by HIV-1. Nature 2003, 422:307-312. 10.1038/nature01470, 12646921.
8. Nowak MA, Anderson RM, McLean AR, Wolfs TF, Goudsmit J, May RM. Antigenic diversity thresholds and the development of AIDS. Science 1991, 254:963-969. 10.1126/science.1683006, 1683006.
9. Wolinsky SM, Kunstman KJ, Safrit JT, Koup RA, Neumann AU, Korber BT. Response: HIV-1 Evolution and Disease Progression. Science 1996, 274:1010-1011. 10.1126/science.274.5289.1010, 17798610.
10. Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, Gupta P, Rinaldo CR, Learn GH, He X, et al. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol 1999, 73:10489-10502. 113104, 10559367.
11. Bagnarelli P, Mazzola F, Menzo S, Montroni M, Butini L, Clementi M. Host-specific modulation of the selective constraints driving human immunodeficiency virus type 1 env gene evolution. J Virol 1999, 73:3764-3777. 104154, 10196271.
12. Freel SA, Fiscus SA, Pilcher CD, Menezes P, Giner J, Patrick E, Lennox JL, Hicks CB, Eron JJ, Shugars DC. Envelope diversity, coreceptor usage and syncytium-inducing phenotype of HIV-1 variants in saliva and blood during primary infection. Aids 2003, 17:2025-2033. 10.1097/00002030-200309260-00003, 14502005.
13. Delwart E, Magierowska M, Royz M, Foley B, Peddada L, Smith R, Heldebrant C, Conrad A, Busch M. Homogeneous quasispecies in 16 out of 17 individuals during very early HIV-1 primary infection. Aids 2002, 16:189-195. 10.1097/00002030-200201250-00007, 11807302.
14. Gottlieb GS, Heath L, Nickle DC, Wong KG, Leach SE, Jacobs B, Gezahegne S, van 't WA, Jacobson LP, Margolick JB, Mullins JI. HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study. J Infect Dis 2008, 197:1011-1015. 10.1086/529206, 18419538.
15. Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, et al. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci USA 2008, 105:7552-7557. 10.1073/pnas.0802203105, 2387184, 18490657.
16. Learn GH, Muthui D, Brodie SJ, Zhu T, Diem K, Mullins JI, Corey L. Virus population homogenization following acute human immunodeficiency virus type 1 infection. J Virol 2002, 76:11953-11959. 10.1128/JVI.76.23.11953-11959.2002, 136917, 12414937.
17. Ritola K, Pilcher CD, Fiscus SA, Hoffman NG, Nelson JA, Kitrinos KM, Hicks CB, Eron JJ, Swanstrom R. Multiple V1/V2 env variants are frequently present during primary infection with human immunodeficiency virus type 1. J Virol 2004, 78:11208-11218. 10.1128/JVI.78.20.11208-11218.2004, 521858, 15452240.
18. Frost SD, Liu Y, Pond SL, Chappey C, Wrin T, Petropoulos CJ, Little SJ, Richman DD. Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J Virol 2005, 79:6523-6527. 10.1128/JVI.79.10.6523-6527.2005, 1091710, 15858036.
19. Rong R, Gnanakaran S, Decker JM, Bibollet-Ruche F, Taylor J, Sfakianos JN, Mokili JL, Muldoon M, Mulenga J, Allen S, et al. Unique mutational patterns in the envelope alpha 2 amphipathic helix and acquisition of length in gp120 hypervariable domains are associated with resistance to autologous neutralization of subtype C human immunodeficiency virus type 1. J Virol 2007, 81:5658-5668. 10.1128/JVI.00257-07, 1900276, 17360739.
20. Coetzer M, Cilliers T, Papathanasopoulos M, Ramjee G, Karim SA, Williamson C, Morris L. Longitudinal analysis of HIV type 1 subtype C envelope sequences from South Africa. AIDS Res Hum Retroviruses 2007, 23:316-321. 10.1089/aid.2006.0207, 17331039.
21. Ping LH, Nelson JA, Hoffman IF, Schock J, Lamers SL, Goodman M, Vernazza P, Kazembe P, Maida M, Zimba D, et al. Characterization of V3 sequence heterogeneity in subtype C human immunodeficiency virus type 1 isolates from Malawi: underrepresentation of X4 variants. J Virol 1999, 73:6271-6281. 112705, 10400718.
22. Tscherning C, Alaeus A, Fredriksson R, Bjorndal A, Deng H, Littman DR, Fenyo EM, Albert J. Differences in chemokine coreceptor usage between genetic subtypes of HIV-1. Virology 1998, 241:181-188. 10.1006/viro.1997.8980, 9499793.
23. Ball SC, Abraha A, Collins KR, Marozsan AJ, Baird H, Quinones-Mateu ME, Penn-Nicholson A, Murray M, Richard N, Lobritz M, et al. Comparing the ex vivo fitness of CCR5-tropic human immunodeficiency virus type 1 isolates of subtypes B and C. J Virol 2003, 77:1021-1038. 10.1128/JVI.77.2.1021-1038.2003, 140829, 12502818.
24. Abraha A, Nankya IL, Gibson R, Demers K, Tebit DM, Johnston E, Katzenstein D, Siddiqui A, Herrera C, Fischetti L, et al. CCR5- and CXCR4-tropic subtype C human immunodeficiency virus type 1 isolates have a lower level of pathogenic fitness than other dominant group M subtypes: implications for the epidemic. J Virol 2009, 83:5592-5605. 10.1128/JVI.02051-08, 2681953, 19297481.
25. Rong R, Li B, Lynch RM, Haaland RE, Murphy MK, Mulenga J, Allen SA, Pinter A, Shaw GM, Hunter E, et al. Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways. PLoS Pathog 2009, 5:e1000594. 10.1371/journal.ppat.1000594, 2741593, 19763269.
26. Kiepiela P, Leslie AJ, Honeyborne I, Ramduth D, Thobakgale C, Chetty S, Rathnavalu P, Moore C, Pfafferott KJ, Hilton L, et al. Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature 2004, 432:769-775. 10.1038/nature03113, 15592417.
27. Salazar-Gonzalez JF, Bailes E, Pham KT, Salazar MG, Guffey MB, Keele BF, Derdeyn CA, Farmer P, Hunter E, Allen S, et al. Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. J Virol 2008, 82:3952-3970. 10.1128/JVI.02660-07, 2293010, 18256145.
28. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
29. Posada D, Crandall KA. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818. 10.1093/bioinformatics/14.9.817, 9918953.
30. Rambaut A. FigTree v1.1.2. 2008, http://tree.bio.ed.ac.uk/software/figtree
31. Drummond A, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007, 7:214. 10.1186/1471-2148-7-214, 2247476, 17996036.
32. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007, 24:1596-1599. 10.1093/molbev/msm092, 17488738.
33. Korber B, Myers G. Signature pattern analysis: a method for assessing viral sequence relatedness. AIDS Res Hum Retroviruses 1992, 8:1549-1560. 10.1089/aid.1992.8.1549, 1457200.
34. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13:555-556.
35. Pond SL, Frost SD, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics 2005, 21:676-679. 10.1093/bioinformatics/bti079, 15509596.
36. Diskin R, Marcovecchio PM, Bjorkman PJ. Structure of a clade C HIV-1 gp120 bound to CD4 and CD4-induced antibody reveals anti-CD4 polyreactivity. Nat Struct Mol Biol 17:608-613. 10.1038/nsmb.1796, 2949298, 20357769.
37. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res 2003, 31:3381-3385. 10.1093/nar/gkg520, 168927, 12824332.
38. Weissenhorn W, Dessen A, Harrison SC, Skehel JJ, Wiley DC. Atomic structure of the ectodomain from HIV-1 gp41. Nature 1997, 387:426-430. 10.1038/387426a0, 9163431.
39. DeLano W. The PyMOL Molecular Graphics System. 2006, 2006. DeLano Scientific, San Carlos, CA, USA.
40. Sagar M, Wu X, Lee S, Overbaugh J. Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity. J Virol 2006, 80:9586-9598. 10.1128/JVI.00141-06, 1617272, 16973562.
41. Huang W, Toma J, Fransen S, Stawiski E, Reeves JD, Whitcomb JM, Parkin N, Petropoulos CJ. Coreceptor tropism can be influenced by amino acid substitutions in the gp41 transmembrane subunit of human immunodeficiency virus type 1 envelope protein. J Virol 2008, 82:5584-5593. 10.1128/JVI.02676-07, 2395220, 18353956.
42. Yang W, Bielawski JP, Yang Z. Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J Mol Evol 2003, 57:212-221. 10.1007/s00239-003-2467-9, 14562964.
43. Zwick MB, Jensen R, Church S, Wang M, Stiegler G, Kunert R, Katinger H, Burton DR. Anti-human immunodeficiency virus type 1 (HIV-1) antibodies 2F5 and 4E10 require surprisingly few crucial residues in the membrane-proximal external region of glycoprotein gp41 to neutralize HIV-1. J Virol 2005, 79:1252-1261. 10.1128/JVI.79.2.1252-1261.2005, 538539, 15613352.
44. Mani I, Gilbert P, Sankale JL, Eisen G, Mboup S, Kanki PJ. Intrapatient diversity and its correlation with viral setpoint in human immunodeficiency virus type 1 CRF02_A/G-IbNG infection. J Virol 2002, 76:10745-10755. 10.1128/JVI.76.21.10745-10755.2002, 136616, 12368317.
45. McNearney T, Hornickova Z, Markham R, Birdwell A, Arens M, Saah A, Ratner L. Relationship of human immunodeficiency virus type 1 sequence heterogeneity to stage of disease. Proc Natl Acad Sci USA 1992, 89:10247-10251. 10.1073/pnas.89.21.10247, 50315, 1438212.
46. Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A, Margolick J, Vlahov D, Quinn T, Farzadegan H, Yu XF. Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci USA 1998, 95:12568-12573. 10.1073/pnas.95.21.12568, 22871, 9770526.
47. Gray ES, Moore PL, Choge IA, Decker JM, Bibollet-Ruche F, Li H, Leseka N, Treurnicht F, Mlisana K, Shaw GM, et al. Neutralizing antibody responses in acute human immunodeficiency virus type 1 subtype C infection. J Virol 2007, 81:6187-6196. 10.1128/JVI.00239-07, 1900112, 17409164.
48. Menzo S, Sampaolesi R, Vicenzi E, Santagostino E, Liuzzi G, Chirianni A, Piazza M, Cohen OJ, Bagnarelli P, Clementi M. Rare mutations in a domain crucial for V3-loop structure prevail in replicating HIV from long-term non-progressors. Aids 1998, 12:985-997. 10.1097/00002030-199809000-00004, 9662194.
49. Gaschen B, Taylor J, Yusim K, Foley B, Gao F, Lang D, Novitsky V, Haynes B, Hahn BH, Bhattacharya T, Korber B. Diversity considerations in HIV-1 vaccine selection. Science 2002, 296:2354-2360. 10.1126/science.1070441, 12089434.
50. Derdeyn CA, Decker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, Denham SA, Heil ML, Kasolo F, Musonda R, Hahn BH, et al. Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 2004, 303:2019-2022. 10.1126/science.1093137, 15044802.
51. Rong R, Bibollet-Ruche F, Mulenga J, Allen S, Blackwell JL, Derdeyn CA. Role of V1V2 and other human immunodeficiency virus type 1 envelope domains in resistance to autologous neutralization during clade C infection. J Virol 2007, 81:1350-1359. 10.1128/JVI.01839-06, 1797511, 17079307.
52. Liu Y, Curlin ME, Diem K, Zhao H, Ghosh AK, Zhu H, Woodward AS, Maenza J, Stevens CE, Stekler J, et al. Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B viruses. Virology 2008, 374:229-233. 10.1016/j.virol.2008.01.029, 2441482, 18314154.
53. Lynch RM, Shen T, Gnanakaran S, Derdeyn CA. Appreciating HIV type 1 diversity: subtype differences in Env. AIDS Res Hum Retroviruses 2009, 25:237-248. 10.1089/aid.2008.0219, 2853864, 19327047.
54. Gnanakaran S, Lang D, Daniels M, Bhattacharya T, Derdeyn CA, Korber B. Clade-specific differences between human immunodeficiency virus type 1 clades B and C: diversity and correlations in C3-V4 regions of gp120. J Virol 2007, 81:4886-4891. 10.1128/JVI.01954-06, 1900169, 17166900.