Fifteen years of env C2V3C3 evolution in six individuals infected clonally with human immunodeficiency virus type 1

Journal of Medical Virology

Volumn 79, Issue 11, 2007, Pages 1629-1639

  Kupfer, Bernd ^a   Sing, Tobias ^b   Schüffler, Peter ^b   Hall, Rabea ^a   Kurz, Ralf ^a   McKeown, Astrid ^a   Schneweis, Karl Eduard ^a   Eberl, Wolfgang ^c   Oldenburg, Johannes ^a   Brackmann, Hans H ^a   Rockstroh, Jürgen K ^a   Spengler, Ulrich ^a   Däumer, Martin P ^d   Kaiser, Rolf ^d   Lengauer, Thomas ^b   Matz, Bertfried ^a  

^a UNIVERSITY OF BONN   (Germany)

^b MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^c KLINIKUM BRAUNSCHWEIG   (Germany)

^d UNIVERSITY OF COLOGNE   (Germany)

Author keywords

Co receptor usage; Convergent; Divergence; Glycosylation; Same source

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; BLOOD SAMPLING; CD4 LYMPHOCYTE COUNT; CLINICAL ARTICLE; GLYCOSYLATION; HEMOPHILIA B; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; HUMAN TISSUE; IMMUNE RESPONSE; NUCLEOTIDE SEQUENCE; PHYLOGENY; VIRUS LOAD; VIRUS STRAIN;

AMINO ACID SEQUENCE; EVOLUTION, MOLECULAR; GENE PRODUCTS, ENV; GLYCOSYLATION; HEMOPHILIA B; HIV ENVELOPE PROTEIN GP120; HIV INFECTIONS; HIV-1; HUMANS; MOLECULAR SEQUENCE DATA; MUTATION; PEPTIDE FRAGMENTS; PHYLOGENY; RECEPTORS, CCR5; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 34748880883     PISSN: 01466615     EISSN: 10969071     Source Type: Journal    
DOI: 10.1002/jmv.20976     Document Type: Article

References (63)

1. Arnold C, Balfe P, Clewley JP. 1995. Sequence distances between env genes of HIV-1 from individuals infected from the same source: Implications for the investigation of possible transmission chains. Virology 211:198-203.
2. Bagnarelli P, Fiorelli L, Vecchi M, Monachetti A, Menzo S, Clementi M. 2003. Analysis of the functional relationship between V3 loop and gp120 context with regard to human immunodeficiency virus coreceptor usage using naturally selected sequences and different viral backbones. Virology 307:328-340.
3. Balfe P, Simmonds P, Ludlam CA, Bishop JO, Leigh Brown AJ. 1990. Concurrent evolution of human immunodeficiency virus type 1 in patients infected from the same source: Rate of sequence change and low frequency of inactivating mutations. J Virol 64:6221-6233.
4. Balzarini J, Van Laethem K, Hatse S, Froeyen M, Peumans W, Van Damme E. 2005. Carbohydrate-binding agents cause deletions of highly conserved glycosylation sites in HIV gp120. J Biol Chem 280:41005-41014.
5. Balzarini J, Van Laethem K, Peumans WJ, Van Damme EJ, Bolmstedt A, Gago F, Schols D. 2006. Mutational pathways, resistance profile, and side effects of cyanovirin relative to human immunodeficiency virus type 1 strains with N-glycan deletions in their gp120 envelopes. J Virol 80:8411-8421.
6. Bonhoeffer S, Holmes EC, Nowak MA. 1995. Causes of HIV diversity. Nature 376:125.
7. Burton DR, Desrosiers RC, Doms RW, Koff WC, Kwong PD, Moore JP, Nabel GJ, Sodroski J, Wilson IA, Wyatt RT. 2004. HIV vaccine design and the neutralizing antibody problem. Nat Immunol 5:233-236.
8. Cheng-Mayer C, Quiroga M, Tung JW, Dina D, Levy JA. 1990. Viral determinants of human immunodeficiency virus type 1 T-cell or macrophage tropism, cytopathogenicity, and CD4 antigen modulation. J Virol 64:4390-4398.
9. Chesebro B, Wehrly K, Nishio J, Perryman S. 1996. Mapping of independent V3 envelope determinants of human immunodeficiency virus type 1 macrophage tropism and syncytium formation in lymphocytes. J Virol 70:9055-9059.
10. Choe H, Farzan M, Sun Y, Sullivan N, Rollins B, Ponath BD, Wu L, Mackay CR, LaRosa G, Newman W, Gerard N, Gerard C, Sodroski J. 1996. The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell 85:1135-1148.
11. Cichutek K, Norley S, Linde R, Kreuz W, Gahr M, Lower J, von Wangenheim G, Kurth R. 1991. Lack of HIV-1 V3 region sequence diversity in two haemophiliac patients infected with a putative biologic clone of HIV-1. AIDS 5:1185-1187.
12. Cichutek K, Merget H, Norley S, Linde R, Kreuz W, Gahr M, Kurth R. 1992. Development of a quasispecies of human immunodeficiency virus type 1 in vivo. Proc Natl Acad Sci USA 89:7365-7369.
13. Clevestig P, Pramanik L, Leitner T, Ehrnst A. 2006. CCR5 use by human immunodeficiency virus type 1 is associated closely with the gp120 V3 loop N-linked glycosylation site. J Gen Virol 87:607-612.
14. Delwart EL, Pan H, Sheppard HW, Wolpert D, Neumann AU, Korber B, Mullins JI. 1997. Slower evolution of human immunodeficiency virus type 1 quasispecies during progression to AIDS. J Virol 71: 7498-7508.
15. Domingo E, Holland JJ. 1997. RNA virus mutations and fitness for survival. Annu Rev Microbiol 51:151-178.
16. Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
17. Fouchier RA, Groenink M, Kootstra NA, Tersmette M, Huisman HG, Miedema F, Schuitemaker H. 1992. Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. J Virol 66:3183-3187.
18. Frost SD, Wrin T, Smith DM, Kosakovsky Pond SL, Liu Y, Paxinos E, Chappey C, Galovich J, Beauchaine J, Petropoulos CJ, Little SJ, Richman DD. 2005. Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc Natl Acad Sci USA 102:18514-18519.
19. Gorny MK, Conley AJ, Karwowska S, Buchbinder A, Xu JY, Emini EA, Koenig S, Zolla-Pazner S. 1992. Neutralization of diverse human immunodeficiency virus type 1 variants by an anti-V3 human monoclonal antibody. J Virol 66:7538-7542.
20. Gorny MK, Revesez K, Williams C, Volsky B, Louder MK, Anyangwe CA, Krachmarov C, Kayman SC, Pinter A, Nadas A, Nyambi PN, Mascola JR, Zolla-Pazner S. 2004. The V3 loop is accessible on the surface of most human immunodeficiency virus type 1 primary isolates and serves as a neutralization epitope. J Virol 78:2394-2404.
21. Ho DD, Neumann AU, Perelson AS, Chen W, Leonard JM, Markowitz M. 1995. Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 373:123-126.
22. Hoffman TL, Doms RW. 1999. HIV-1 envelope determinants for cell tropism and chemokine receptor use. Mol Membr Biol 16: 57-65.
23. Holmes EC, Zhang LQ, Simmonds P, Ludlam CA, Leigh Brown AJ. 1992. Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc Natl Acad Sci USA 89:4835-4839.
24. Hutto C, Zhou Y, He J, Geffin R, Hill M, Scott W, Wood C. 1996. Longitudinal studies of viral sequence, viral phenotype, and immunologic parameters of human immunodeficiency virus type 1 infection in perinatally infected twins with discordant disease courses. J Virol 70:3589-3598.
25. Hwang SS, Boyle TJ, Lyerly HK, Cullen BR. 1991. Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science 253:71-74.
26. Jensen MA, van't Wout AB. 2003. Predicting HIV-1 coreceptor usage with sequence analysis. AIDS Rev 5:104-112.
27. Kasper P, Kaiser R, Kleim JP, Oldenburg J, Brackmann HH, Rockstroh J, Schneweis KE. 1993. Diversification of HIV-1 strains after infection from a unique source. AIDS Res Hum Retroviruses 9:153-157.
28. Kasper P, Kaiser R, Oldenburg J, Brackmann HH, Matz B, Schneweis KE. 1994. Parallel evolution in the V3 region of HIV type 1 after infection of hemophiliacs from a homogeneous source. AIDS Res Hum Retroviruses 10:1669-1678.
29. Kasper P, Simmonds P, Schneweis KE, Kaiser R, Matz B, Oldenburg J, Brackmann HH, Holmes EC. 1995. The genetic diversification of the HIV type 1 gag p17 gene in patients infected from a common source. AIDS Res Hum Retroviruses 11:1197-1201.
30. Kasturi L, Chen H, Shakin-Eshleman SH. 1997. Regulation of N-linked core glycosylation: Use of a site-directed mutagenesis approach to identify Asn-Xaa-Ser/Thr sequons that are poor oligosaccharide acceptors. Biochem J 323:415-419.
31. Kleim JP, Bailly E, Schneweis KE, Brackmann HH, Hammerstein U, Hanfland P, van Loo B, Oldenburg J. 1990. Acute HIV-1 infection in patients with haemophilia B treated with beta-propiolactone-UV-inactivated clotting factor. Thromb Haemost 64:336-337.
32. Kleim JP, Ackermann A, Brackmann HH, Gahr M, Schneweis KE. 1991. Epidemiologically closely related viruses from hemophilia B patients display high homology in two hypervariable regions of the HIV-1 env gene. AIDS Res Hum Retroviruses 7:417-421.
33. Kupfer B, Oldenburg J, Brackmann HH, Matz B, Schneweis KE, Kaiser R. 1995. Beta-propiolactone UV inactivated clotting factor concentrate is the source of HIV-infection of 8 hemophilia B patients: Confirmed. Thromb Haemost 74:1386-1387.
34. Kupfer B, Kaiser R, Rockstroh JK, Matz B, Schneweis KE. 1998. Role of HIV-1 phenotype in viral pathogenesis and its relation to viral load and CD4+ T-cell count. J Med Virol 56:259-263.
35. Lehmann C, Däumer M, Boussaad I, Sing T, Beerenwinkel N, Lengauer T, Schmeisser N, Wyen C, Fätkenheuer G, Kaiser R. 2006. Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART. J Clin Virol 37:300-304.
36. Lemey P, Derdelinckx I, Rambaut A, Van Laethem K, Dumont S, Vermeulen S, Van Wijngaerden E, Vandamme A. 2005. Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain. J Virol 79:11981-11989.
37. Liu SL, Schacker T, Musey L, Shriner D, McElrath MJ, Corey L, Mullins JI. 1997. Divergent patterns of progression to AIDS after infection from the same source: Human immunodeficieny virus type 1 evolution and antiviral responses. J Virol 71:4284-4295.
38. Marshall RD. 1974. The nature and metabolism of the carbohydrate-peptide linkages of glycoproteins. Biochem Soc Symp 40:17-26.
39. McCaffrey RA, Saunders C, Hensel M, Stamatatos L. 2004. N-linked glycosylation of the V3 loop and the immunologically silent face of gp120 protects human immunodeficiency virus type 1 SF162 from
40. neutralization by anti-gp120 and anti-gp41 antibodies. J Virol 78:3279-3295.
41. Mellquist JL, Kasturi L, Spitalnik L, Shakin-Eshleman SH. 1998. The amino acid following an Asn-X-Ser/Thr sequon is an important determinant of N-linke core glycosylation efficiency. Biochemistry 37:6833-6837.
42. Page RDM. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357-358.
43. Pollakis G, Kang S, Kliphuis A, Chalaby MIM, Goudsmit J, Paxton WA. 2001. N-linked glycosylation of the HIV type-1 gp120 envelope glycoprotein as a major determinant of CCR5 and CXCR4 coreceptor utilization. J Biol Chem 276:13433-13441.
44. Polzer S, Dittmar MT, Schmitz H, Schreiber M. 2002. The N-linked glycan g15 with the V3 loop of the HIV-1 external glycoprotein gp120 affects coreceptor usage, cellular tropism, and neutralization. Virology 304:70-80.
45. Resch W, Hoffman N, Swanstrom R. 2001. Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 using neural networks. Virology 288:51-62.
46. Ross HA, Rodrigo AG. 2002. Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J Virol 76:11715-11720.
47. Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
48. Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, Gupta P, Rinaldo CR, Learn GH, He X, Huang XL, Mullins JI. 1999. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol 73:10489-10502.
49. Simmonds P, Balfe P, Ludlam CA, Bishop JO, Leigh 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.
50. Speck RF, Wehrly K, Piatt EJ, Atchison RE, Charo IF, Kabat D, Chesebro B, Goldsmith MA. 1997. Selective employment of chemokine receptors as human immunodeficiency virus type 1 coreceptors determined by individual amino acids within the envelope V3 loop. J Virol 71:7136-7139.
51. Stephens HAF. 2005. HIV-1 diversity versus HLA class I polymorphism. Trends Immunol 26:41-47.
52. Templeton AR, Reichert RA, Weisstein AE, Yu XF, Markham RB. 2004. Selection in context: Patterns of natural selection in the glycoprotein 120 region of human immunodeficiency virus type 1 within infected individuals. Genetics 167:1547-1561.
53. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882.
54. Tugarinov V, Zvi A, Levy R, Hayek Y, Matsushita S, Anglister J. 2000. NMR structure of an anti-gp120 antibody complex with a V3 peptide reveals a surface important for co-receptor binding. Structure 8:385-395.
55. Watkins BA, Buge S, Aldrich K, Davis AE, Robinson J, Reitz MS, Jr, Robert-Guroff M. 1996. Resistance of human immunodeficiency virus type 1 to neutralization by natural antisera occurs through single amino acid substitutions that cause changes in antibody binding at multiple sites. J Virol 70:8431-8437.
56. Wei X, Ghosh SK, Taylor ME, Johnson VA, Emini EA, Deutsch P, Lifson JD, Bonhoeffer S, Nowak MA, Hahn BH, Saag MS, Shaw GM. 1995. Viral dynamics in human immunodeficiency virus type 1 infection. Nature 373:117-122.
57. Wei X, Decker JM, Wang S, Hui H, Kappes JC, Wu X, Salazar-Gonzalez JF, Salazar MG, Kilby JM, Saag MS, Komarova NL, Nowak MA, Hahn BH, Kwong D, Shaw GM. 2003. Antibody neutralization and escape by HIV-1. Nature 422:307-312.
58. Williamson S, Perry SM, Bustamente CD, Orive ME, Stearns MN, Kelly JK. 2005. A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients. Mol Biol Evol 22:456-468.
59. Yamaguchi Y, Gojobori T. 1997. Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts. Proc Natl Acad Sci USA 94:1264-1269.
60. Ye Y, Si ZH, Moore JP, Sodroski J. 2000. Association of structural changes in the V2 and V3 loops of the gp120 envelope glycoprotein with acquisition of neutralization resistance in a simian-human immunodeficiency virus passaged in vivo. J Virol 74:11955-11962.
61. Zhang L, Diaz RS, Ho DD, Mosley JW, Busch MP, Mayer A. 1997. Host-specific driving force in human immunodeficiency virus type 1 evolution in vivo. J Virol 71:2555-2561.
62. Zhang M, Gaschen B, Blay W, Foley B, Haigwood N, Kuiken C, Korber B. 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.
63. Zolla-Pazner S, Zhong P, Revesz K, Volsky B, Williams C, Nyambi P, Gorny MK. 2004. The cross-clade neutralizing activity of a human monoclonal antibody is determined by the GPGR V3 motif of HIV type 1. AIDS Res Hum Retroviruses 20:1254-1258.