Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis

Proceedings of the National Academy of Sciences of the United States of America

Volumn 93, Issue 20, 1996, Pages 10864-10869

  Leitner, Thomas ^a   Escanilla, David ^b   Franzén, Christer ^c   Uhlén, Mathias ^d   Albert, Jan ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b UNIVERSITY OF CHILE   (Chile)

^c Kärnsjukhuset ^*  (Sweden)

^d ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT;

ARTICLE; BLOOD SAMPLING; CALCULATION; DIAGNOSTIC ACCURACY; DNA SEQUENCE; GENE EXPRESSION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; PHYLOGENY; PRIORITY JOURNAL; T LYMPHOCYTE; VIRUS TRANSMISSION;

AMINO ACID SEQUENCE; BASE SEQUENCE; FEMALE; GENES, ENV; GENES, GAG; HIV INFECTIONS; HIV-1; HUMANS; MALE; METHODS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, VIRAL;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0029744336     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.93.20.10864     Document Type: Article

References (46)

1. Cann, R. L., Stoneking, M. & Wilson, A. C. (1987) Nature (London) 325, 31-36.
2. Ou, C. Y., Ciesielski, C. A., Myers, G., Bandea, C. I., Luo, C. C., Korber, B. T., Mullins, J. I., Schochetman, G., Berkelman, R. L., Economou, A. N., Witte, J. J., Furman, L. J., Satten, G. A., MacInnes, K. A., Curran, J. W., Jaffe, H. W. & Laboratory Investigation Group and Epidemiologic Investigation Group (1992) Science 256, 1155-1161.
3. Holmes, E. C., Zhang, L. Q., Simmonds, P., Rogers, A. S. & Brown, A. J. (1993) J. Infect. Dis. 167, 1411-1414.
4. Albert, J., Wahlberg, J., Leitner, T., Escanilla, D. & Uhlén, M. (1994) J. Virol. 68, 5918-5924.
5. Holmes, E. C., Zhang, L. Q., Robertson, P., Cleland, A., Harvey, E., Simmonds, P. & Leigh-Brown, A. J. (1995) J. Infect. Dis. 171, 45-53.
6. Myers, G., Korber, B., Wain-Hobson, S., Jeang, K.-T., Henderson, L. E. & Pavlakis, G. N. (1994) Human Retroviruses and AIDS (Los Alamos Natl. Lab., Los Alamos, NM).
7. DeBry, R. W., Abele, L. G., Weiss, S. H., Hill, M. D., Bouzas, M., Lorenzo, E., Graebnitz, F. & Resnick, L. (1993) Nature (London) 361, 691.
8. Holmes, E. C., Leigh Brown, A. J. & Simmonds, P. (1993) Nature (London) 364, 766.
9. Felsenstein, J. (1988) Annu. Rev. Genet. 22, 521-565.
10. Swofford, D. L. & Olsen, G. J. (1990) in Molecular Systematics, eds. Hillis, D. M. & Moritz, C. (Sinauer, Sunderland, MA), pp. 411-501.
11. Nei, M. (1991) in Phylogenetic Analysis of DNA Sequences, eds. Miyamoto, M. M. & Cracraft, J. (Oxford Univ. Press, New York), pp. 90-128.
12. Hillis, D. M., Huelsenbeck, J. P. & Cunningham, C. W. (1994) Science 264, 671-677.
13. Nei, M., Takezaki, N. & Sitnikova, T. (1995) Science 267, 253-255.
14. Sourdis, J. & Nei, M. (1988) Mol. Biol. Evol. 5, 298-311.
15. Saitou, N. & Imanishi, T. (1989) Mol. Biol. Evol. 6, 514-525.
16. Saitou, N. (1988) J. Mol. Evol. 27, 261-273.
17. Hillis, D. M., Bull, J. J., White, M. E., Badgett, M. R. & Molineux, I. J. (1992) Science 255, 589-592.
18. Gojobori, T., Moriyama, E. N. & Kimura, M. (1990) Proc. Natl. Acad. Sci. USA 87, 10015-10018.
19. Schreck, F., Bromage, T. G., Betzler, C. G., Ring, U. & Juwayeyi, Y. M. (1993) Nature (London) 365, 833-836.
20. Franzén, C., Albert, J., Biberfeld, G., Lidin-Janson, G. & Lowhagen, G. B. (1988) Fourth International Conference on AIDS (Int. Conf. on AIDS, Stockholm), abstr. 4021.
21. Leitner, T., Halapi, E., Scarlatti, G., Rossi, P., Albert, J., Fenyö, E. M. & Uhlén, M. (1993) BioTechniques 15, 120-126.
22. Leitner, T., Escanilla, D., Marquina, S., Wahlberg, J., Broström, C., Hansson, H. B., Uhlén, M. & Albert, J. (1995) Virology 209, 136-146.
23. Hultman, T., Bergh, S., Moks, T. & Uhlén, M. (1991) BioTechniques 10, 84-93.
24. Fitch, W. M. & Margoliash, E. (1967) Science 155, 279-284.
25. Saitou, N. & Nei, M. (1987) Mol. Biol. Evol. 4, 406-425.
26. Rzhetsky, A. & Nei, M. (1993) Mol. Biol. Evol. 10, 1073-1095.
27. Felsenstein, J. (1993) PHYLIP: Phylogeny Inference Package (Univ. of Washington, Seattle), Version 3.52c.
28. Eck, R. V. & Dayhoff, M. O. (1966) Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found., Silver Spring, MD).
29. Sneath, P. H. A. & Sokal, R. R. (1973) Numerical Taxonomy (Freeman, San Francisco).
30. Jukes, T. H. & Cantor, C. R. (1969) in Mammalian Protein Metabolism, ed. Munro, H. N. (Academic, New York), pp. 21-132.
31. Kimura, M. (1980) J. Mol. Evol. 16, 111-120.
32. Rzhetsky, A. & Nei, M. (1994) METREE: Program Package for Inferring and Testing Minimum Evolution Trees (Inst. Mol. Evol. Genet., Pennsylvania State Univ., PA), Version 1.4.
33. Swofford, D. L. (1991) PAUP: Phylogenetic Analysis Using Parsimony (Ill. Natl. Hist. Surv., Champaign, IL), Version 3.1.1
34. Maddison, W. P. & Maddison, D. R. (1992) MACCLADE: Analysis of Phylogeny and Character Evolution (Sinauer, Sunderland, MA), Version 3.04.
35. Estabrook, G. F., McMorris, F. R. & Meacham, C. A. (1985) Syst. Zool. 34, 193-200.
36. Robinson, D. F. & Foulds, L. R. (1991) Math. Biosci. 53, 105-147.
37. Page, R. D. M. (1993) COMPONENT (Biogeography and Conservation Lab., Natural History Museum, London), Version 2.0.
38. Felsenstein, J. (1985) Evolution 39, 783-791.
39. Hills, D. M. & Huelsenbeck, J. P. (1992) J. Hered. 83, 189-195.
40. Rzhetsky, A. & Nei, M. (1992) Mol. Biol. Evol. 9, 945-967.
41. Strunnikova, N., Ray, S. C., Livingston, R. A., Rubalcaba, E. & Viscidi, R. P. (1995) J. Virol. 69, 7548-7558.
42. Zhang, L. Q., MacKenzie, P., Cleland, A., Holmes, E. C., Brown, A. J. & Simmonds, P. (1993) J. Virol. 67, 3345-3356.
43. Doolittle, R. F. (1994) Trends Biochem. Sci. 19, 15-18.
44. Wolinsky, S. M., Wike, C. M., Korber, B. T., Hutto, C., Parks, W. P., Rosenblum, L. L., Kunstman, K. J., Furtado, M. R. & Munoz, J. L. (1992) Science 255, 1134-1137.
45. Robertson, D. L., Sharp, P. M., McCutchan, F. E. & Hahn, B. H. (1995) Nature (London) 374, 124-126.
46. Vartanian, J., Meyerhans, A., Sala, M. & Wain-Hobson, S. (1994) Proc. Natl. Acad. Sci. USA 91, 3092-3096.