Covariability of V3 loop amino acids

AIDS Research and Human Retroviruses

Volumn 12, Issue 15, 1996, Pages 1401-1411

  Bickel, P J ^a   Cosman, P C ^b   Olshen, R A ^c   Spector, P C ^a   Rodrigo, A G ^d   Mullins, J I ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c STANFORD LAW SCHOOL   (United States)

^d UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS ENVELOPE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; GENETIC LINKAGE; GENETIC VARIABILITY; HUMAN IMMUNODEFICIENCY VIRUS 1; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

EID: 0029849837     PISSN: 08892229     EISSN: None     Source Type: Journal    
DOI: 10.1089/aid.1996.12.1401     Document Type: Article

References (23)

1. Korber BTM, Farber RM, Wolpert DH, and Lapedes AS: Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis. Proc Natl Acad Sci USA 1993;90:7176-7180.
2. Myers G, Korber BTM, Berzofsky JA, Smith RF, and Pavlakis GF (eds): Human Retroviruses and AIDS. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 1991.
3. Davis D, Stephens M, Willers C, and Lachmann PJ: Glycosylation governs the binding of antipeptide antibodies to regions of hypervariable amino acid sequence within recombinant gp120 of human immunodeficiency virus type 1. J Gen Virol 1990;71:2889-2898.
4. Korber B, Wolinsky S, Haynes B, Kunstman K, Levy R, Furtado M, Otto P, and Myers G: HIV-1 intrapatient sequence diversity in the immunogenic V3 region. AIDS Res Hum Retroviruses 1992;8:1461-1465.
5. Hwang SS, Boyle TJ, Lyerly HK, and Cullen BR: Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science 1992;253:71-74.
6. de Jong J-J, Goudsmit J, Keulen W, Klaver B, Krone W, Tersmette M, and de Ronde A: 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.
7. Chesebro B, Wehrly K, Nishio J, and Ferryman S: Macrophagetropic human immunodeficiency virus isolates from different patients exhibit unusual V3 envelope sequence homogeneity in comparison with T-cell-tropic isolates: Definition of critical amino acids involved in cell tropism. J Virol 1992;66:6547-6554.
8. Fouchier RAM, Groenink M, Kootstra NA, Termsette M, Huisman HG, Miedema F, and Schuitemaker H: Phenotype-associated sequence variation I the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. J Virol 1992;66: 3183-3187.
9. Westervelt P, Trowbridge DB, Epstein LG, Blumberg BM, Li Y, Hahn BH, Shaw GM, Price RW, and Ratner L: Macrophage tropism determinants of human immunodeficiency virus type 1 in vivo. J Virol 1992;66:2577-2582.
10. Milich L, Margolin B, and Swanstrom R: V3 loop of the human immunodeficiency virus type 1 Env protein: Interpreting sequence variability. J Virol 1993;67:5623-5634.
11. Seiller-Moiseiwitsch F, Margolin BH, and Swanstrom R: Genetic variability of the human immunodeficiency virus. Annu Rev Genet 1994;28:559-596.
12. Cosman PC, Gray RM, and Olshen RA: Evaluating quality of compressed medical images: SNR, subjective rating, and diagnostic accuracy. Proc IEEE 1994;82(6):919-932.
13. Breiman L, Friedman JM, Olshen RA, and Stone C: Classification and Regression Trees. Wadsworth, Belmont, California, 1984.
14. Myers G, Korber B, Wain-Hobson S, Smith RF, and Parlakis GN: Human Retroviruses and AIDS. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 1993.
15. Kuiken CL, Zwart G, Gaan E, Coutinho RA, van der Hoek JAR, and 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.
16. LaRosa GJ, Davide JP, Weinhold K, Waterbury JA, Profy AT, Lewis JA, Langlois AJ, Dresman GR, Boswell RN, Shadduck P, Holley LH, Karplus M, Bolognesi DP, Mathews TJ, Emini EA, and Putney SD: Conserved sequence and structural elements in the HIV-1 principal neutralizing determinant Science 1990;249:932-935.
17. Goodman LA and Kruskal WH: Measures of association for Cross Classification. Springer-Verlag, New York, 1979.
18. Weir BS and Cockerham CC: Testing hypotheses about linkage disequilibrium with multiple alleles. Genetics 1978;88:633-642.
19. Everitt BS: Analysis of Contingency Tables, 2nd Ed. Chapman & Hall, London, 1992, pp. 37-40.
20. Wain-Hobson S: Is antigenic variation of HIV important for AIDS and what might be expected in the future? In: The Evolutionary Biology of Viruses (Morse S, ed.). Raven Press, New York, 1994.
21. Ghiara JB, Stura EA, Stanfield RL, Profy AT, and Wilson IA: Crystal structure of the principal neutralization site of HIV 1. Science 1994;264:82-85.
22. Goodman LA: Some multiplicative models for the analysis of cross classified data. In: Proc. VIth Berkeley Symposium on Math. Statistics and Probability (LeCam L, et al., eds.), Vol. 1. University of California Press, Berkeley, California, 1972, pp. 649-696.
23. Agresti A: Categorical Data Analysis. John Wiley & Sons, New York, 1992.