Evidence for limited within-person evolution of the V3 domain of the HIV-1 envelope in the Amsterdam population

AIDS

Volumn 10, Issue 1, 1996, Pages 31-37

  Kuiken, Carla L ^a   Lukashov, Vladimir V ^a   Baan, Elly ^a   Dekker, John ^a   Leunissen, Jack A M ^b   Goudsmit, Jaap ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

Author keywords

Evolution; Molecular epidemiology; V3 domain; Variation

Indexed keywords

VIRUS RNA;

ARTICLE; CONSENSUS SEQUENCE; DRUG ABUSE; EVOLUTION; GENE SEQUENCE; HOMOSEXUALITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; MAJOR CLINICAL STUDY; MALE; NETHERLANDS; PRIORITY JOURNAL; SEROCONVERSION; VIRION; VIRUS ENVELOPE;

EID: 0030042078     PISSN: 02699370     EISSN: None     Source Type: Journal    
DOI: 10.1097/00002030-199601000-00005     Document Type: Article

References (56)

1. Kuiken CL, Korber BTM: Epidemiological significance of intra- and inter-person variation of HIV-1. AIDS 1994, 8 (suppl 1): S73-S83.
2. Hillis DM, Huelsenbeck JP: Support for dental HIV transmission. Nature 1994, 369:24-25.
3. Ciesielsky CA, Marianos D, Ou CY, et al.: Transmission of human immunodeficiency virus in a dental practice. Ann Intern Med 1992, 166:798-805.
4. Ou CY, Ciesielsky CA, Myers G, et al.: Molecular epidemiology of HIV transmission in a dental practice. Science 1992, 256:1165-1171.
5. Smith TF, Waterman MS: The continuing case of the Florida dentist. Science 1992, 256:1155-1156.
6. DeBry RW, Abele LG, Welss SH, et al.: Dental HIV transmission [letter]. Nature 1993, 361:691.
7. Albert J, Wahlberg J, Uhlen M: Forensic evidence by DNA sequencing. Nature 1993, 361:595-596.
8. McNearney T, Hornickova Z, Kloster B, et al.: Evolution of sequence diversity among human immunodeficiency virus type 1 isolates derived from a blood donor and a recipient. Pediatr Res 1993, 33:36-42.
9. Wolfs TFW, Zwart G, Bakker M, Goudsmit J: HIV-1 genomic RNA diversification following sexual and parenteral virus transmission. Virology 1992, 189:103-110.
10. Burger H, Weiser B, Flaherty K, Gulla J, Nguyen P-N, Gibbs RA: Evolution of human immunodeficiency virus type 1 nucleotide sequence diversity among close contacts. Proc Natl Acad Sci USA 1991, 88:11236-11240.
11. Mulder-Kampinga GA, Kuiken CL, Dekker J, Scherpbier HJ, Boer K, Goudsmit J: Genomic HIV-1 RNA variation in mother and child following intra-uterine virus transmission. J Gen Virol 1993, 74:1747-1756.
12. Scarlatti G, Leitner T, Halapi E, et al.: Comparison of variable region 3 sequences of human immunodeficiency virus type 1 from infected children with RNA and DNA sequences of the virus populations of their mothers. Proc Natl Acad Sci USA 1993, 90:1721-1725.
13. Weiser B, Burger H, Nachman S, Hsu YJ, Gibbs R: Use of serial HIV-1 sequences from a pregnant woman and her twins to study timing of vertical transmission. Vaccines 1993, 131-136.
14. Wolinsky SM, Wike CM, Korber B, et al.: Selective transmission of human immunodeficiency virus type 1 variants from mothers to infants. Science 1992, 255:1134-1137.
15. Albert J, Wahlberg J, Leitner T, Escanilla D, Uhlen M: Analysis of a rape case by direct sequencing of the human immunodeficiency virus type 1 pol and gag genes. J Virol 1994, 68:5918-5924.
16. Holmes EC, Zhang LQ, Simmonds P, Rogers AS, Leigh Brown AJ: Molecular investigation of human immunodeficiency virus (HIV) infection in a patient of an HIV-infected surgeon. J Infect Dis 1993, 167:1411-1414.
17. Lamers S, Sleasman JW, Xiong She J, et al.: Independent variation and positive selection in env V1 and V2 domains within maternal-infant strains of human immunodeficiency virus type 1 in vivo. J Virol 1993, 67:3951-3960.
18. Simmonds P, Balfe P, Ludlam CA, Bishop JO, Leigh Brown AJ: Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1. J Virol 1990, 64:5840-5850.
19. Shioda T, Levy JA, Cheng-Mayer C: Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of human immunodeficiency virus type 1. Proc Natl Acad Sci USA 1992, 89:9434-9438.
20. Hwang SS, Boyle TJ, Lyerly HK, Cullen BR: Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science 1991, 253:71-74.
21. Grimaila R, Fuller BA, Rennert PD, et al.: Mutations in the principal neutralization determinant of human immunodeficiency virus type 1 affect syncytium formation, virus infectivity, growth kinetics, and neutralization. J Virol 1992, 66:1875-1883.
22. Freed EO, Myers DJ, Risser R: Identification of the principal neutralizing determinant of human immunodeficiency virus type 1 as a fusion domain. J Virol 1991, 65:190-194.
23. De Jong JJ, Goudsmit J, Keulen W, et al.: Human immunodeficiency virus type 1 clones chimeric for the envelope V3 domain differ in syncytium formation and replication capacity. J Virol 1992, 66:757-765.
24. Fouchier RAM, Groenink M, Kootstra NA, et al.: Phenotype-associated sequence variation in the third variable region of the human immunodeficiency virus type 1 gp120 molecule. J Virol 1992, 66:3183-3187.
25. Javaherian K, Langlois AJ, LaRosa GJ, et al.: Broadly neutralizing antibodies elicited by the hypervariable neutralizing determinant in HIV-1. Science 1990, 250:1590-1593.
26. Goudsmit J, Debouck C, Meloen RH, et al.: Human immunodeficiency virus type 1 neutralization epitope with conserved architecture elicits early type-specific antibodies in experimentally infected chimpanzees. Proc Natl Acad Sci USA 1988, 85:4478-4482.
27. Takahashi H, Nakagawa Y, Pendleton CD, et al.: Induction of broadly cross-reactive cytotoxic T cells recognizing an HIV-1 envelope determinant. Science 1992, 255:333-336.
28. Clerici M, Lucey DR, Zajac RA, et al.: Detection of cytotoxic T lymphocytes specific for synthetic peptides of gp160 in HIV-seropositive individuals. J Immunol 1991, 146:2214-2219.
29. Hart MK, Palker TJ, Matthews TJ, et al.: Synthetic peptides containing T and B cell epitopes from human immunodeficiency virus envelope gp120 induce anti-HIV proliferative responses and high titers of neutralizing antibodies in rhesus monkeys. J Immunol 1990, 145:2677-2685.
30. Pinter A, Honnen WJ, Tilley SA: Conformational changes affecting the V3 and CD4-binding domains of human immunodeficiency virus type 1 gp120 associated with env processing and with binding of ligands to these sites. J Virol 1993, 67:5692-5697.
31. McKeating JA, Cordell J, Dean C, Balfe P: Synergistic interaction between ligands binding to the CD4 binding site and V3 domain of human immunodeficiency virus type 1 gp120. Virology 1992, 191:732-742.
32. Travis BM, Dykers TI, Hewgill D, et al.: Functional roles of the V3 hypervariable region of HIV-1 gp160 in the processing of gp160 and the formation of syncytia in CD4+ cells. Virol 1992, 186:313-317.
33. Wyatt R, Thali M, Tilley S, et al.: Relationship of the human immunodeficiency virus type 1 gp120 third variable loop to a component of the CD4 binding site in the fourth conserved region. J Virol 1992, 66:6997-7004.
34. Moore JP, Nara PL: The role of the V3 domain of gp120 in HIV infection. AIDS 1991, 5 (suppl 2):S21-S33.
35. Sattentau QJ, Moore JP: Conformational changes induced in the human immunodeficiency virus envelope glycoprotein by soluble CD4 binding. J Exp Med 1991, 174:407-415.
36. Skinner MA, Langlois AJ, McDanal CB, McDougal S, Bolognesi DP, Matthews TJ: Neutralizing antibodies to an immunodominant envelope sequence do not prevent gp120 binding to CD4. J Virol 1988, 62:4195-4200.
37. De Wolf F, Goudsmit J, Paul DA, et al.: Risk of AIDS-related complex and AIDS in homosexual men with persistent HIV antigenaemia. BMJ 1987, 295:569-572.
38. Van den Hoek JAR, Coutinho RA, Van Haastrecht HJA, Van Zadelhoff AW, Goudsmit J: Prevalence and risk factors of HIV infections among drug users and drug-using prostitutes in Amsterdam. AIDS 1988, 2:55-60.
39. Coutinho RA, Lelie N, Albrecht-van Lent P, et al.: Efficacy of a heat-inactivated hepatitis B vaccine in male homosexuals: outcome of a placebo-controlled double blind trial. BMJ 1983, 286:1305-1308.
40. Coutinho RA, Krone WJA, Smit L, et al.: Introduction of lymphadenopathy associated virus or human T lymphotropic virus (LAV/HTLV-III) into the male homosexual community in Amsterdam. Genitourin Med 1986, 62:38-43.
41. Boom R, Sol CJA, Salimans MMM, Jansen CL, Wertheimvan Dillen PME, Van der Noordaa J: A rapid and simple method for purification of nucleic acids. J Clin Microbiol 1990, 28:495-503.
42. Kuiken CL, Zwart G, Baan E, Coutinho RA, Van den Hoek JAR, Goudsmit J: Increasing antigenic and genetic diversity of the HIV-1 V3 domain in the course of the AIDS epidemic. Proc Natl Acad Sci USA 1993, 90:9061-9065.
43. De Wolf F, Hogervorst E, Goudsmit J, et al.: Syncytium-inducing (SI) and non-syncytium-inducing (NSI) capacity of human immunodeficiency virus type 1 (HIV-1) subtypes other than B: phenotypic and genotypic characteristics. AIDS Res Hum Retroviruses 1994, 10:1387-1400.
44. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-425.
45. Felsenstein J: PHYLIP Manual, Version 3.5. Berkeley: University of California; 1993.
46. Kimura M: A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J Mol Evol 1980, 16:111-120.
47. Nei M, Gojobori T: Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986, 3:418-426.
48. Kumar S, Tamura K, Nei M: MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. CABIOS 1994, 10:189-192.
49. Korber B, Myers G: Signature patterns analysis: a method for assessing viral sequence relatedness. AIDS Res Hum Retroviruses 1992, 8:1549-1558.
50. Van Haastrecht HJA, Van den Hoek JAR, Mientjes GHC, Coutinho RA: Did the introduction of HIV among homosexual men precede the introduction of HIV among injecting drug users in The Netherlands? [Letter]. AIDS 1992, 6:131-132.
51. Higgins DG: Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets. CABIOS 1992, 8:15-22.
52. Kuiken CL, Nieselt-Struwe K, Weiller GF, Goudsmit J: Quasispecies behavior of HIV-1: a sample analysis of sequence data. In Methods in Molecular Genetics, Vol 4: Molecular Virology. Edited by Adolph KW. Orlando: Academic Press; 1994:100-119.
53. Zhang LQ, MacKenzie P, Cleland A, Holmes EC, Leigh Brown AJ, Simmonds P: Selection for specific sequences in the external envelope protein of HIV-1 upon primary infection. J Virol 1993, 67:3345-3356.
54. Shpaer EG, Delwart EL, Kuiken CL, Goudsmit J, Bachmann MH, Mullins JI: Conserved V3 loop sequences and the transmission of human immunodeficiency virus type 1. AIDS Res Hum Retroviruses 1994, 10:1679-1684.
55. Zhu T, Mo H, Wang N, et al.: Genotypic and phenotypic characterization of HIV-1 in patients with primary infection. Science 1993, 261:1179-1181.
56. Kuiken CL, Goudsmit J: Silent mutation pattern in V3 sequences distinguishes virus according to risk group in Europe. AIDS Res Hum Retroviruses 1994, 10:319-320.